Abstract:
:Fourier transform infrared (FTIR) spectroscopy was applied to the blue-light photoreceptor photoactive yellow protein (PYP) to investigate water structural changes possibly involved in the photocycle of PYP. Photointermediates were stabilized at low temperature, and difference IR spectra were obtained between intermediate states and the original state of PYP (pG). Water structural changes were never observed in the >3570 cm(-)(1) region for the intermediates stabilized at 77-250 K, such as the red-shifted pR and blue-shifted pB intermediates. In contrast, a negative band was observed at 3658 cm(-)(1) in the pB minus pG spectrum at 295 K, which shifts to 3648 cm(-)(1) upon hydration with H(2)(18)O. The high frequency of the O-H stretch of water indicates that the water O-H group does not form hydrogen bonds in pG, and newly forms these upon pB formation at 295 K, but not at 250 K. Among 92 water molecules in the crystal structure of PYP, only 1 water molecule, water-200, is present in a hydrophobic core inside the protein. The amide N-H of Gly-7 and the imidazole nitrogen atom of His-108 are its possible hydrogen-bonding partners, indicating that one O-H group of water-200 is free to form an additional hydrogen bond. The water band at 3658 cm(-)(1) was indeed diminished in the H108F protein, which strongly suggests that the water band originates from water-200. Structural changes of amide bands in pB were much greater in the wild-type protein at 295 K than at 250 K or in the H108F protein at 295 K. The position of water-200 is >15 A remote from the chromophore. Virtually no structural changes were reported for regions larger than a few angstroms away from the chromophore, in the time-resolved X-ray crystallography experiments on pB. On the basis of the present results, as well as other spectroscopic observations, we conclude that water-200 (buried in a hydrophobic core in pG) is exposed to the aqueous phase upon formation of pB in solution. In neither crystalline PYP nor at low temperature is this structural transition observed, presumably because of the restrictions on global structural changes in the protein under these conditions.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Kandori H,Iwata T,Hendriks J,Maeda A,Hellingwerf KJdoi
10.1021/bi000357fsubject
Has Abstractpub_date
2000-07-11 00:00:00pages
7902-9issue
27eissn
0006-2960issn
1520-4995pii
bi000357fjournal_volume
39pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::The formation and role of arachidonic acid (AA) and its metabolites during gonadotropin releasing hormone- (GnRH-) induced gonadotropin secretion were investigated in primary cultures of rat pituitary cells. Prelabeled cells ([3H]AA) responded to GnRH challenge with increased formation (about 2-fold) of the leukotrien...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00139a004
更新日期:1992-06-23 00:00:00
abstract::The inhibitory potency of 3'-azido-3'-deoxythymidine 5'-triphosphate (AZTTP) against HIV-1 reverse transcriptase (HIV-1 RT) has been further evaluated. The results indicate that the previously reported low Ki values for AZTTP against HIV-1 RT (2.35 nM) are due neither to the to the direct tight binding of AZTTP to HIV...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00120a013
更新日期:1992-02-11 00:00:00
abstract::Incubation of bovine plasma amine oxidase (BPAO) with benzylamine and various p-substituted analogues results in a time-dependent inactivation that is attributable to buildup of the H(2)O(2)-turnover product on the basis of protection afforded by coincubation with catalase. The mechanism of inactivation is distinct fr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi002118y
更新日期:2001-01-23 00:00:00
abstract::The expression of the transforming gene product of Rous sarcoma virus (pp60v-src) in Saccharomyces cerevisiae has recently been reported (Kornbluth et al., 1987; Brugge et al., 1987). To carry out biochemical and structural studies of this enzyme, a facile purification was developed. The purification was accomplished ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00449a013
更新日期:1989-11-14 00:00:00
abstract::A method has been developed for the routine synthesis of 2'(3')-o-monoacyl ribonucleoside 5'-diphosphates for stepwise synthesis of oligoribonucleotides with Escherichia coli polynucleotide phosphorylase. The use of triethyl orthoisovalerate allows the facile preparation of 2'(3')-o-isovaleryl-UDP, -CDP, -ADP, -GDP, -...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00675a027
更新日期:1975-02-25 00:00:00
abstract::This study highlights the effect of incorporation of locked nucleic acid (LNA) on improving the functional efficacy of DNAzymes against microRNAs (antagomirzymes). DNAzymes were designed against two different sites of miR-27a, which were encompassed both within the precursor and mature form of miRNA. The cleavage and ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi101185k
更新日期:2010-11-09 00:00:00
abstract::The infectious isoform of the prion protein (PrPSc) is derived from cellular PrP (PrPC) in a conversion reaction involving a dramatic reorganization of secondary and tertiary structure. While our understanding of the pathogenic role of PrPSc has grown, the normal physiologic function of PrPC still remains unclear. Usi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi972827k
更新日期:1998-05-19 00:00:00
abstract::The oxidation of alcohol to aldehyde by horse liver alcohol dehydrogenase (LADH) requires the transfer of a hydride ion from the alcohol substrate to the cofactor nicotinamide adenine dinucleotide (NAD). A quantum mechanical tunneling contribution to this hydride transfer step has been demonstrated in a number of LADH...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi973184b
更新日期:1998-06-30 00:00:00
abstract::The mechanism of binding of reduced 1-(2-carboxyphenylamino)-1-deoxyribulose 5-phosphate (rCdRP) to two different binding sites on the bifunctional enzyme is determined by kinetic studies, using temperature-jump and stopped-flow equipment with fluorescence detection. Two rapid binding processes and a comparatively slo...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00593a030
更新日期:1979-12-25 00:00:00
abstract::Chemical-modification studies on submitochondrial particle pyridine dinucleotide transhydrogenase (EC 1.6.1.1) demonstrate the presence of one class of sulfhydryl group in the nicotinamide adenine dinucleotide phosphate (NADP) site and another peripheral to the active site. Reaction of the peripheral sulfhydryl group ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00615a015
更新日期:1978-10-31 00:00:00
abstract::Activation enthalpies and entropies are reported for proton-deuteron exchange at 42 amide sites in T4 lysozyme and compared with activation volumes for the same residues obtained earlier [Hitchens, T. K., and Bryant, R. G. (1998) Biochemistry 37, 5878-5887]. There is no correlation found between activation volume and ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi991718y
更新日期:2000-01-11 00:00:00
abstract::A novel and efficient enzyme kinetics assay using electrospray ionization mass spectrometry was developed and applied to the bacterial carbohydrate sulfotransferase (NodST). NodST catalyzes the sulfuryl group transfer from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to chitobiose, generating 3'-phosphoadenosine 5'-ph...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi020457g
更新日期:2002-11-05 00:00:00
abstract::Cytochrome bo from Escherichia coli is a ubiquinol oxidase which is a member of the superfamily of heme-copper respiratory oxidases. This superfamily, which includes the eukaryotic cytochrome c oxidases, has in common a bimetallic center consisting of a high-spin heme component and a copper atom (CuB) which is the sit...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00092a029
更新日期:1993-10-19 00:00:00
abstract::Lon is a homo-oligomeric ATP-dependent serine protease that functions in the degradation of damaged and certain regulatory proteins. This enzyme has emerged as a novel target in the development of antibiotics because of its importance in conferring bacterial virulence. In this study, we explored the mechanism by which...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi7002789
更新日期:2007-06-05 00:00:00
abstract::The effects of various ginsenosides on calmodulin-dependent phosphodiesterase isozymes have been investigated. Ginsenosides were found to be potent inhibitors of bovine heart calmodulin-dependent phosphodiesterase and the 60-kDa isozyme of bovine brain calmodulin-dependent phosphodiesterase but not of the 63-kDa isozy...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00070a001
更新日期:1993-05-18 00:00:00
abstract::We have labeled the primer binding domain of murine leukemia virus reverse transcriptase (MuLV RT) by covalently cross-linking 5' end labeled d(T)8 to MuLV RT, using ultraviolet light energy. The specificity and the functional significance of the primer cross-linking reaction were demonstrated by the fact that (i) oth...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00240a014
更新日期:1991-07-02 00:00:00
abstract::Animal galectins (lectins with specificity for beta-galactosides of glycan chains) are potent effectors in diverse aspects of cell sociology. Gene divergence has led to different groups and a marked interspecies variability in the number of members per group. Since the suitability of a model for studying functionality...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi900083q
更新日期:2009-05-26 00:00:00
abstract::Escherichia coli 16S RNA from 30S ribosomal subunits was isolated, oxidized at the 3' end, and labeled with the thiosemicarbazide derivatives of fluorescein or eosin. Labeled 16S RNA was reconstituted into 30S subunits. They were almost fully active compared to 30S subunits reconstituted from unlabeled 16S RNA by usin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00521a033
更新日期:1981-09-01 00:00:00
abstract::Malic enzyme from pigeon liver is alkylated by the substrate analogue bromopyruvate, resulting in the concomitant loss of its oxidative decarboxylase and oxalacetate decarboxylase activities, but not its ability to reduce alpha-keto acids. The inactivation of oxidative decarboxylase activity follows saturation kinetic...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00621a024
更新日期:1977-01-25 00:00:00
abstract::To better understand origin recognition and initiation of DNA replication, we have examined by NMR complexes formed between the origin-binding domain of SV40 T antigen (T-ag-obd), the initiator protein of the SV40 virus, and cognate and noncognate DNA oligomers. The results reveal two structural effects associated wit...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi030228+
更新日期:2004-06-08 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::Splicing factor RBM10 and its close homologues RBM5 and RBM6 govern the splicing of oncogenes such as Fas, NUMB, and Bcl-X. The molecular architecture of these proteins includes zinc fingers (ZnFs) and RNA recognition motifs (RRMs). Three of these domains in RBM10 that constitute the RNA binding part of this splicing ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.7b01242
更新日期:2018-03-13 00:00:00
abstract::Formiminotransferase-cyclodeaminase denatured in 6 M guanidine hydrochloride (Gdn.HCl) refolds and reassembles to the native octameric structure upon dilution into buffer. Both enzymic activities are recovered to greater than 90%, and the renatured enzyme "channels" the formiminotetrahydropteroylpentaglutamate interme...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00409a042
更新日期:1988-05-03 00:00:00
abstract::Single-tryptophan-containing mutants of low adenylation state Escherichia coli glutamine synthetase (wild type has two tryptophans at positions 57 and 158) have been constructed and studied by multifrequency phase/modulation fluorescence spectroscopy. The W57L mutant (retains tryptophan at residue 158) and the W158S m...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00228a008
更新日期:1991-04-09 00:00:00
abstract::The complete amino acid sequence of the major component myoglobin from Amazon River dolphin, Inia geoffrensis, was determined by specific cleavage of the protein to obtain large peptides which are readily degraded by the automatic sequencer. Three easily separable peptides were obtained by cleaving the protein with cy...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00695a018
更新日期:1975-12-02 00:00:00
abstract::S100A1, a member of the S100 protein family, is an EF-hand containing Ca(2+)-binding protein (93 residues per subunit) with noncovalent interactions at its dimer interface. Each subunit of S100A1 has four alpha-helices and a small antiparallel beta-sheet consistent with two helix-loop-helix calcium-binding domains [Ba...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0118308
更新日期:2002-01-22 00:00:00
abstract::Two-dimensional nuclear magnetic resonance techniques were used to assign the NH, C alpha H, and C beta H protons of over 60 of the 104 amino acid residues in the 1H NMR spectrum of horse ferrocytochrome c. The majority of these amino acids were completely assigned. Assignments were based on the analysis of two-dimens...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00341a002
更新日期:1985-09-24 00:00:00
abstract::Chloride intracellular channel protein 1 (CLIC1) functions as an anion channel in plasma and nuclear membranes when its soluble monomeric form converts to an integral-membrane form. The transmembrane region of CLIC1 is located in its thioredoxin-like domain 1, but the mechanism whereby the protein converts to its memb...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9010607
更新日期:2009-09-08 00:00:00
abstract::The flexibility and curvature of duplex DNAs containing mismatched sites have been monitored as a function of temperature. The diffusion coefficients are dependent on the flexibility and the curvature of the DNA, and these have been determined by NMR-based methods. The diffusion coefficients, D, depend on a Boltzmann ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9916630
更新日期:2000-01-11 00:00:00
abstract::Resonance Raman (RR) spectra of soluble guanylate cyclase (sGC) reported by five independent research groups have been classified as two types: sGC(1) and sGC(2). Here we demonstrate that the RR spectra of sGC isolated from bovine lung contain only sGC(2) while both species are observed in the spectra of the CO-bound ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0489208
更新日期:2005-01-25 00:00:00