Abstract:
:RecA-catalyzed DNA recombination is initiated by a mandatory, high-energy form of DNA in RecA-nucleoprotein filaments, where bases are highly unstacked and the backbone is highly unwound. Interestingly, only the energetics consequent to adenosine triphosphate (ATP) binding, rather than its hydrolysis, seems sufficient to mediate such a high-energy structural hallmark of a recombination filament. The structural consequence of ATP hydrolysis on the DNA part of the filament thus remains largely unknown. We report time-resolved fluorescence dynamics of bases in RecA-DNA complexes and demonstrate that DNA bases in the same exhibit novel, motional dynamics with a rotational correlation time of 7-10 ns, specifically in the presence of ATP hydrolysis. When the ongoing ATP hydrolysis of RecA-DNA filament is "poisoned" by a nonhydrolyzable form of ATP (ATPgammaS), the motional dynamics cease and reveal a global motion with a rotational correlation time of >20 ns. Such ATP hydrolysis-induced flexibility ensues in single-stranded as well as double-stranded bases of RecA-DNA filaments. These results suggest that the role of ATP hydrolysis is to induce a high level of backbone flexibility in RecA-DNA filament, a dynamic property that is likely to be important for efficient strand exchanges in ATP hydrolysis specific RecA reactions. It is the absence of these motions that may cause high rigidity in RecA-DNA filaments in ATPgammaS. Dynamic light scattering measurement comparisons of RecA-ss-DNA filaments formed in ATPgammaS vs that of ATP confirmed such an interpretation, where the former showed a complex of larger (30 nm) hydrodynamic radius than that of latter (12-15 nm). Taken together, these results reveal a more dynamic state of DNA in RecA-DNA filament that is hydrolyzing ATP, which encourage us to model the role of ATP hydrolysis in RecA-mediated DNA transactions.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Ramreddy T,Sen S,Rao BJ,Krishnamoorthy Gdoi
10.1021/bi034667ksubject
Has Abstractpub_date
2003-10-21 00:00:00pages
12085-94issue
41eissn
0006-2960issn
1520-4995journal_volume
42pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Intracellular reduction of carcinogenic Cr(VI) generates Cr-DNA adducts formed through the coordination of Cr(III) to DNA phosphates (phosphotriester-type adduct). Here, we examined the role of Cr(III)-DNA adducts in mutagenesis induced by metabolism of Cr(VI) with cysteine. Reduction of Cr(VI) caused a strong oxidati...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0015459
更新日期:2001-01-16 00:00:00
abstract::Energy coupling factor (ECF) transporters take up micronutrients in Bacteria and Archaea. They consist of a membrane-embedded S-component that provides substrate specificity and a three-subunit ECF module that couples ATP hydrolysis to transport. The S-components ThiT (for thiamin) and NiaX (for niacin) from Lactococc...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b00609
更新日期:2015-08-11 00:00:00
abstract::In the DNA recognition mode of C(2)H(2)-type zinc fingers, the finger-finger connection region, consisting of the histidine spacing (HX(3-5)H) and linker, would be important for determining the orientation of the zinc finger domains. To clarify the influence of spacing between two ligand histidines in the DNA binding,...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi035999s
更新日期:2004-05-25 00:00:00
abstract::Myotoxin a from the venom of Crotalus viridis viridis (prairie rattlesnake) is a small protein which is responsible for myonecrosis. It is a basic protein with 42 amino acid residues of known sequence. Three disulfide bonds give it a highly compact structure. Microscopic examination of the toxin's effects reveals that...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00347a021
更新日期:1985-12-17 00:00:00
abstract::Apolipoprotein AIV is one of the principal apolipoproteins synthesized by the rat small intestine. We have cloned a cDNA encoding a portion of preapolipoprotein AIV mRNA. A kinetically fractionated cDNA probe highly enriched for the abundant intestinal mucosal mRNA sequences was used to screen a library of recombinant...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00265a007
更新日期:1982-10-26 00:00:00
abstract::Rapid withdrawal of estrogen from immature chicks, previously stimulated with the hormone, results in the inhibition of transcription of mRNAs of egg white proteins, rapid degradation of existing estrogen-induced mRNAs of egg white proteins, and decline in ribosomes and weight of the oviduct. On rapid withdrawal of es...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00409a019
更新日期:1988-05-03 00:00:00
abstract::Members of the phospholipase C-beta (PLC-beta) family of proteins are activated either by G alpha or G beta gamma subunits of heterotrimeric G proteins. To define specific regions of PLC-beta 3 that are involved in binding and activation by G beta gamma, a series of fragments of PLC-beta 3 as glutathione-S-transferase...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi992021f
更新日期:2000-02-22 00:00:00
abstract::The carbohydrate binding specificity of the seed lectin from Artocarpus integrifolia, artocarpin, has been elucidated by the enzyme-linked lectin absorbent assay [Misquith, S., et al (1994) J. Biol. Chem. 269, 30393-30401], wherein it was demonstrated to be a Man/Glc specific lectin with high affinity for the trisacch...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi000744p
更新日期:2000-09-05 00:00:00
abstract::P1,P2-Bidentate Co(NH3)4PP was found to be a competitive inhibitor of pyrophosphatase vs. MgPP (Kis = 8.7 mM, pH 7) and, in the presence of Mg2+, an active substrate as well. P1,P2-Bidentate Cr(III) complexes of pyrophosphate, imidodiphosphate, and methylenediphosphonate were also competitive inhibitors vs. MgPP (pH 5...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00517a021
更新日期:1981-07-07 00:00:00
abstract::Thioacetamide, a hepatocarcinogen and an inhibitor of heme synthesis, blocks the phenobarbitone-mediated increase in the transcription of cytochrome P-450b+e messenger RNA in rat liver. This property is also shared by CoCl2 and 3-amino-1,2,4-triazole, two other inhibitors of heme synthesis. Thus, it appears feasible t...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00364a009
更新日期:1986-08-12 00:00:00
abstract::Ornithine decarboxylase (ODC) is a pyridoxal 5'-phosphate (PLP) dependent homodimeric enzyme. It is a recognized drug target against African sleeping sickness, caused by Trypanosoma brucei. One of the currently used drugs, alpha-difluoromethylornithine (DFMO), is a suicide inhibitor of ODC. The structure of the T. bru...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9915115
更新日期:1999-11-16 00:00:00
abstract::For many different enveloped viruses the crystal structure of the fusion protein core has been established. A striking conservation in the tertiary and quaternary arrangement of these core structures is repeatedly revealed among members of diverse families. It has been proposed that the primary role of the core involv...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0255322
更新日期:2002-04-09 00:00:00
abstract::The structure of a short-chain IgG2a antibody, which is a member of the family of mouse anti-dansyl switch variant antibodies with identical variable regions but different heavy-chain constant regions [Dangl, J.L., Parks, D. R., Oi, V. T., & Herzenberg, L. A. (1982) Cytometry 2, 395-401], is reported. Amino acid seque...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00476a013
更新日期:1990-06-19 00:00:00
abstract::Bacillus thuringiensis (Bt) insecticidal toxins bind to receptors on midgut epithelial cells of susceptible insects, and binding triggers biochemical events that lead to insect mortality. Recently, a 100-kDa aminopeptidase N (APN) was isolated from brush border membrane vesicles (BBMV) of Anopheles quadrimaculatus and...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi801181g
更新日期:2008-10-28 00:00:00
abstract::Protein-protein interactions such as those between small G proteins and their effector proteins control most cell signaling pathways and thereby govern many cellular processes in both normal and disease states. Each small G protein interacts with several effectors, some shared between similar G proteins and others uni...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi701539x
更新日期:2007-12-11 00:00:00
abstract::In experiments designed to characterize the basis of amyloid fibril stability through mutational analysis of the Abeta (1-40) molecule, fibrils exhibit consistent, significant structural malleability. In these results, and in other properties, amyloid fibrils appear to more resemble plastic materials generated from sy...
journal_title:Biochemistry
pub_type: 杂志文章,评审
doi:10.1021/bi0620959
更新日期:2007-01-09 00:00:00
abstract::Catalysis by glycogen phosphorylase involves a mechanism in which binding of one substrate tightens the binding of the other substrate to produce a productive ternary enzyme-substrate complex. In this work the molecular basis for this synergism is probed in crystallographic studies on ternary complexes in which the gl...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi960072w
更新日期:1996-06-11 00:00:00
abstract::The annexin fold consists of four 70-residue domains with markedly homologous sequences and nearly identical structures. Each domain contains five helices designated A to E. Domain 2 of annexin I was obtained by chemical synthesis including ten specifically labeled residues and studied by 1H-15N NMR and circular dichr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi960747v
更新日期:1996-08-13 00:00:00
abstract::We have established that UvrABC nuclease is equally efficient in cutting mitomycin C (MC)-DNA monoadducts formed at different sequences and that the degree of UvrABC cutting represents the extent of drug-DNA bonding. Using this method we determined the effect of C5 cytosine methylation on the DNA monoalkylation by MC ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi991307h
更新日期:2000-03-14 00:00:00
abstract::Mammalian cGMP- and cAMP-dependent protein kinase show considerable similarity in amino acid sequence, although they specifically bind different cyclic nucleotides. Results of cGMP analogue binding experiments, combined with modeling of the cGMP binding sites by analogy to the structure of the homologous catabolite ge...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00440a059
更新日期:1989-07-11 00:00:00
abstract::Studies utilizing the overexpression of individual isoforms indicated that both PKC-alpha and -delta promote a number of biological effects, including inhibition of DNA synthesis associated with rearrangements of the actin cytoskeleton in the murine B-cell lymphoma (Baf3), differentiation of the murine promyelocyte li...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9731807
更新日期:1998-04-21 00:00:00
abstract::Piscidin 4, an antimicrobial peptide recently isolated from mast cells of hybrid striped bass (Morone chrysops female × Morone saxatilis male), is unusual in that it is twice as long (44 amino acids) as the typical members of the piscidin family. We previously showed that native piscidin 4 had a modified amino acid at...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi101395j
更新日期:2011-04-26 00:00:00
abstract::The molecular structure of ammonium deoxycytidylyl-(3'-5')-deoxyguanosine, crystallized from aqueous acetone near pH 4, was determined for X-ray diffraction data. The crystals were tetragonal, space group P43212 with a = b = 11.078 (1) A and c = 45.826 (4) A. The structure was solved by tangent expansion of phases bas...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00277a014
更新日期:1983-04-12 00:00:00
abstract::Thermostable direct hemolysin (TDH) of Vibrio parahemolyticus is a membrane-damaging pore-forming toxin with potent cytolytic/cytotoxic activity. TDH exists as a tetramer consisting of protomers with a core β-sandwich domain, flanked by an 11-amino acid long N-terminal region (NTR). This NTR could not be modeled in th...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.9b00937
更新日期:2020-02-04 00:00:00
abstract::The mobility of vesicular stomatitis virus (VSV) G protein on the surface of infected BHK cells was studied by using the technique of fluorescence photobleaching recovery. The fraction of surface G protein that was mobile in that time scale of the measurement (minutes) was at least 75%, a relatively high value among c...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00508a047
更新日期:1981-03-03 00:00:00
abstract::Ketosteroid isomerase (KSI) is one of the most proficient enzymes catalyzing an allylic isomerization reaction at a diffusion-controlled rate. In this study of KSI, we have detailed the structures of its active site, the role of various catalytic residues, and have explained the origin of the its fast reactivity by ca...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi001629h
更新日期:2000-11-14 00:00:00
abstract::The calcitonin/CGRP gene pre-mRNA is alternatively spliced in a tissue-specific manner resulting in the formation of calcitonin mRNA in thyroid C-cells and CGRP mRNA in neurons. Computer analysis of the RNA containing the 3' splice acceptor of the calcitonin-specific exon 4 predicts that this region has the potential ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9808058
更新日期:1998-11-10 00:00:00
abstract::The heterodimeric actin capping protein (CP) is regulated by a set of proteins that contain CP-interacting (CPI) motifs. Outside of the CPI motif, the sequences of these proteins are unrelated and distinct. The CPI motif and surrounding sequences are conserved within a given protein family, when compared to those of o...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.0c00092
更新日期:2020-03-24 00:00:00
abstract::The DNA strand cleavage reaction catalyzed by endonuclease III from Escherichia coli (endo III) on the 3'-side of aldehyde abasic sites proceeds by a syn beta-elimination involving abstraction of the 2'-pro-S proton and formation of a trans alpha,beta-unsaturated aldose product; we previously reported the same stereoc...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00218a033
更新日期:1991-01-29 00:00:00
abstract::Insulin-stimulated glucose disposal in skeletal muscle proceeds predominantly through a nonoxidative pathway with glycogen synthase as a rate-limiting enzyme, yet the mechanisms for insulin activation of glycogen synthase are not understood despite years of investigation. Isolation of putative insulin second messenger...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0508845
更新日期:2005-08-23 00:00:00