Abstract:
:The dynamic behavior of the rRNA A-site plays an important functional role. We have employed femtosecond time-resolved spectroscopy to investigate the nature of the conformational dynamics. In the drug-free state, the A-site samples multiple distinct conformations. Drug binding shifts the population distribution in a drug-specific manner. Motions of bases on nanosecond and picosecond time scales are differentially affected by the drug binding. Our results underscore the importance of understanding the detailed dynamic picture of molecular recognition by resolving dynamics in the distinct picosecond time regime and facilitate development of antimicrobial drugs targeting dynamic RNAs.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Lu J,Zhao L,Xia A,Xia T,Qi Xdoi
10.1021/bi400053ssubject
Has Abstractpub_date
2013-03-12 00:00:00pages
1651-3issue
10eissn
0006-2960issn
1520-4995journal_volume
52pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Filamin A (FLNA) is a ubiquitously expressed actin cross-linking protein and a scaffold of numerous binding partners to regulate cell proliferation, migration, and survival. FLNA is a homodimer, and each subunit has an N-terminal actin-binding domain followed by 24 immunoglobulin-like repeats (R). FLNA mediates mechan...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.9b00100
更新日期:2019-11-26 00:00:00
abstract::Association of the human papillomavirus (HPV) E2 protein with its palindromic DNA-binding site is a necessary step for transcriptional trans-activation. To study the interaction between DNA and E2, the carboxyl-terminal domain of HPV-11 E2 protein (E2C) was expressed in Escherichia coli and purified to homogeneity. Th...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi960447d
更新日期:1996-07-30 00:00:00
abstract::The ATP-hydrolyzing portion of the proton pump from clathrin-coated vesicles (isolated from calf brain) was solubilized with three nondenaturing detergents (cholate, octyl glucoside, and Triton X-100). The hydrodynamic properties of the solubilized (Mg2+)-ATPase were then determined by sedimentation analysis in H2O an...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00363a015
更新日期:1986-07-29 00:00:00
abstract::Merozoite surface protein 2 (MSP2), an abundant glycosylphosphatidylinositol-anchored protein on the surface of Plasmodium falciparum merozoites, is a promising malaria vaccine candidate. MSP2 is intrinsically disordered and forms amyloid-like fibrils in solution under physiological conditions. The 25 N-terminal resid...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi201880s
更新日期:2012-02-21 00:00:00
abstract::Steroid-receptor complexes formed at low temperature and ionic strength are unable to bind to target cell nuclei. After a temporary exposure to high ionic strength and/or temperature they become activated (i.e., able to bind to nuclei). However, there exists an equilibrium between activated and nonactivated complexes;...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00664a025
更新日期:1976-09-21 00:00:00
abstract::Modified (Arg63-Ile64 reactive-site peptide bond hydrolyzed) soybean trypsin inhibitor (Kunitz) with all reactive amino groups, except that of Ile64, protected was described in the preceding paper (Kowalski, D., and Laskowski, M., Jr. (1976), Biochemistry, preceding paper in this issue). Treatment of this inhibitor wi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00651a022
更新日期:1976-03-23 00:00:00
abstract::A survey of RuvB protein-mediated ATP hydrolysis yields the following observations. (1) The RuvB protein exhibits a DNA-independent ATPase activity with a turnover number (based on a RuvB monomer) approaching 6 min-1 and a Km of 154 microM. Single-stranded DNA and linear duplex DNA have small but significant effects o...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00030a019
更新日期:1995-08-01 00:00:00
abstract::The binding of propidium to poly(dA).poly(dT) [poly(dA.dT)] and to poly[d(A-T)].poly[d(A-T)] [poly[d(A-T)2]] has been compared under a variety of solution conditions by viscometric titrations, binding studies, and kinetic experiments. The binding of propidium to poly[d(A-T)2] is quite similar to its binding to calf th...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00336a029
更新日期:1985-07-16 00:00:00
abstract::All phosphagen kinases contain a conserved cysteine residue which has been shown by crystallographic studies, on both creatine kinase and arginine kinase, to be located in the active site. There are conflicting reports as to whether this cysteine is essential for catalysis. In this study we have used site-directed mut...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi011208f
更新日期:2001-10-02 00:00:00
abstract::A series of promoters with nine base-pair substitutions in the spacer DNA separating the -10 and -35 regions was used to demonstrate that Escherichia coli RNA polymerase is sensitive to events affecting the spacer DNA--a region not directly contacted by the enzyme. The drugs distamycin A and netropsin specifically enh...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00377a040
更新日期:1987-02-10 00:00:00
abstract::The reaction of cytochrome c oxidase (COX) from Rhodobacter sphaeroides with hydrogen peroxide has been studied at alkaline (pH 8.5) and acidic (pH 6.5) conditions with the aid of a stopped-flow apparatus. Absorption changes in the entire 350-800 nm spectral range were monitored and analyzed by a global fitting proced...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi010115v
更新日期:2001-08-14 00:00:00
abstract::The X-ray crystal structures of the complexes of the recombinant kringle 1 domain of human plasminogen (Klpg) with the ligands epsilon-aminocaproic acid (EACA) and trans-4-(aminomethyl)cyclohexane-1-carboxylic acid (AMCHA), which are representative of a class of in vivo antifibrinolytic agents, have been determined at...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9521351
更新日期:1996-02-27 00:00:00
abstract::The interactions of myelin basic protein and peptides derived from it with detergent micelles of lysophosphatidylglycerol, lysophosphatidylserine, palmitoyllysophosphatidic acid, and sodium lauryl sulfate, and with mixed micelles of the neutral detergent dodecylphosphocholine and the negatively charged detergent palmi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00461a014
更新日期:1990-03-06 00:00:00
abstract::The essential active site Fe3+ of protocatechuate 3,4-dioxygenase [3, 4-PCD, subunit structure (alphabetaFe3+)12] is bound by axial ligands, Tyr447 (147beta) and His462 (162beta), and equatorial ligands, Tyr408 (108beta), His460 (160beta), and a solvent OH- (Wat827). Recent X-ray crystallographic studies have shown th...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi972047b
更新日期:1998-02-24 00:00:00
abstract::Here we explore the use of ethidium to determine relative affinities of different gene delivery vectors for DNA and describe an improved method for studying the interaction. Specifically, we investigate the binding of poly(amidoamine) dendrimers and show that the DNA-dendrimer-ethidium system is far from thermodynamic...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi1015887
更新日期:2011-02-22 00:00:00
abstract::The topography of the photosynthetic reaction center (RC) polypeptides (H, M, and L) was investigated by proteolysis and radioiodination of membrane vesicles isolated from Rhodopseudomonas sphaeroides. Chromatophores, obtained from French-pressed cell lysates, are closed vesicles' and oriented inside out with respect ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00519a012
更新日期:1981-08-04 00:00:00
abstract::Nonenzymatic deamidation of asparagine and glutamine in peptides and proteins is a frequent modification both in vivo and in vitro. The biological effect is not completely understood, but it is often associated with protein degradation and loss of biological function. Here we describe the deamidation of CsgA, the majo...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.7b00241
更新日期:2017-06-13 00:00:00
abstract::The recognition sequence of the Myb protein has been recently described to be pyAACKGHH (where py = T/C, K = G/T, and H = A/C/T), modifying the earlier identification as pyAACKG [Ording, E., et al. (1994) Eur. J. Biochem. 222, 113-120]. We had earlier determined the solution structure of the minimal cognate sequence T...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9806753
更新日期:1998-07-14 00:00:00
abstract::This research was undertaken to distinguish between local and global unfolding in the reversible thermal denaturation of bovine pancreatic ribonclease A (RNase A). Local unfolding was monitored by steady-state and time-resolved fluorescence of nine mutants in each of which a single tryptophan was substituted for a wil...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi001945w
更新日期:2001-01-09 00:00:00
abstract::We have studied the structure of the CuB site in the binuclear heme-copper center of the fully oxidized form of the quinol-oxidizing cytochrome aa3-600 from Bacillus subtilis by EXAFS and ENDOR spectroscopy. This enzyme is member of the large superfamily of heme-copper respiratory oxidases, which catalyze the reductio...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00032a019
更新日期:1995-08-15 00:00:00
abstract::Arginine-70 of human dihydrofolate reductase (hDHFR) is a highly conserved residue which X-ray crystallographic data have shown to interact with the alpha-carboxylate of the terminal L-glutamate moiety of either folic acid or methotrexate (MTX). The rationale for this study was to introduce a conservative amino acid r...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00247a005
更新日期:1991-08-20 00:00:00
abstract::The functional diversity of small GTP-binding proteins (G proteins) and their ability to function as molecular switches are based on their interactions with many different proteins. A wealth of structural data has revealed that their partners are often unrelated to each other in sequence and structure, but their bindi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi049630u
更新日期:2004-06-08 00:00:00
abstract::We have combined three mutations previously shown to stabilize lambda repressor against thermal denaturation. Two of these mutations are in helix 3, where Gly-46 and Gly-48 have been replaced by alanines [Hecht, M. H., et al. (1986) Proteins: Struct., Funct., Genet. 1, 43-46]. The other mutation, which replaces Tyr-88...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00419a059
更新日期:1988-09-20 00:00:00
abstract::Retinoid X receptors (RXRs) are transcription factors with important functions in embryonic development, metabolic processes, differentiation, and apoptosis. A particular feature of RXRs is their ability to act as obligatory heterodimerization partners of class II nuclear receptors. At the same time, these receptors a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b01122
更新日期:2016-03-29 00:00:00
abstract::By limited proteolysis of a type kappa immunoglobulin light chain (Oku) with clostripain, both the VL and CL fragments were obtained with a high yield. The unfolding and refolding by guanidine hydrochloride of light chain Oku and its VL and CL fragments were studied at pH 7.5 and 25 degrees C with circular dichroism a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00393a015
更新日期:1987-09-22 00:00:00
abstract::The solution structure of Cucurbita maxima trypsin inhibitor-V (CMTI-V), which is also a specific inhibitor of the blood coagulation protein, factor XIIa, was determined by 1H NMR spectroscopy in combination with a distance-geometry and simulated annealing algorithm. Sequence-specific resonance assignments were made f...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00015a034
更新日期:1995-04-18 00:00:00
abstract::We characterized endocytosis of iron-saturated (holo) and iron-depleted (apo) 125I-labeled bovine lactoferrin (Lf) by isolated rat hepatocytes. Hepatocytes ingested both Lf forms--determined by EGTA/dextran sulfate removal of surface-bound Lf--at maximal endocytic rates of 1.85 and 1.52 fmol cell-1 min-1 for 125I-apo-...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00212a046
更新日期:1993-12-14 00:00:00
abstract::Purine repressor (PurR) binding to specific DNA is enhanced by complexing with purines, whereas lactose repressor (LacI) binding is diminished by interaction with inducer sugars despite 30% identity in their protein sequences and highly homologous tertiary structures. Nonetheless, in switching from low- to high-affini...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0028643
更新日期:2001-07-10 00:00:00
abstract::To identify the residues essential for interfacial binding and substrate binding of human pancreatic phospholipase A2 (hpPLA2), several ionic residues in the putative interfacial binding surface (R6E, K7E, K10E, and K116E) and substrate binding site (D53K and K56E) were mutated. Interfacial affinity of these mutants w...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi990600e
更新日期:1999-06-15 00:00:00
abstract::31P nuclear magnetic resonance (NMR) saturation-transfer (ST) techniques have been used to measure steady-state flows through phosphate-adenosine 5'-triphosphate (ATP) exchange reactions in glucose-grown derepressed yeast. Our results have revealed that the reactions catalyzed by glyceraldehyde-3-phosphate dehydrogena...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00397a043
更新日期:1987-11-17 00:00:00