Abstract：
:Rhodopsin is the photoreceptor in vertebrate rod cells responsible for vision at low light intensities. The photoreactive chromophore in rhodopsin is 11-cis-retinal bound to the protein via a protonated Schiff base with Glu113 as the counterion. We have used the observed 13C NMR chemical shifts of the conjugated retinal carbons in combination with semiempirical molecular orbital calculations to establish the major charge interactions in the retinal binding site of rhodopsin and its primary photoproduct, bathorhodopsin. In rhodopsin, the NMR data constrain one of the carboxylate oxygens (O1) of Glu113 to be approximately 3 A from the C12 position of the retinal with the second oxygen oriented away from the conjugated retinal chain. The O1-C12-H angle is constrained by taking into account the 500 nm absorption maximum of the protein-bound retinal as well as the chemical shift data. The bathorhodopsin retinal binding site structure is generated from the rhodopsin model by isomerization of the C11 = C12 bond and incorporation of C-C single bond twists from C8 to C15. The resulting structure yields a moderate fit to both the chemical shift data and the 543 nm absorption maximum of bathorhodopsin. In both the rhodopsin and bathorhodopsin models, we have included a structural water molecule hydrogen bonded with the Schiff base to account for the high C = N stretching vibrations previously observed.(ABSTRACT TRUNCATED AT 250 WORDS)
journal_name
Biochemistryjournal_title
Biochemistryauthors
Han M,Smith SOdoi
10.1021/bi00004a037subject
Has Abstractpub_date
1995-01-31 00:00:00pages
1425-32issue
4eissn
0006-2960issn
1520-4995journal_volume
34pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:Aristolochene synthase, a metal-dependent sesquiterpene cyclase from Aspergillus terreus, catalyzes the ionization-dependent cyclization of farnesyl diphosphate (FPP) to form the bicyclic eremophilane (+)-aristolochene with perfect structural and stereochemical precision. Here, we report the X-ray crystal structure of...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi400691v
更新日期：2013-08-13 00:00:00
abstract：:Fluoroaluminate and fluoroberyllate are potent inhibitors of the ATPase activity of myosin. Inhibition requires the presence of ADP, and much evidence has accumulated to suggest that the tetrahedral fluoroaluminate and fluoroberyllate ions act as phosphate analogues, binding with high affinity at the active site in th...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00090a022
更新日期：1993-10-05 00:00:00
abstract：:Polylysine promoted extensive membrane mixing of liposomes only if the buffer pH was below the pKa of the lysyl residues. This observation suggested that fusion could be regulated in a physiological pH range if the homopolymer of L-histidine was substituted as fusogen. Microgram quantities of polyhistidine were added ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00322a001
更新日期：1985-01-01 00:00:00
abstract：:Imidazole glycerol phosphate synthase (ImGPS) from Thermotoga maritima is a model enzyme for studying allostery. The ImGPS complex consists of the cyclase subunit HisF and the glutaminase subunit HisH whose activity is stimulated by substrate binding to HisF in a V-type manner. To investigate the significance of a put...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.0c00332
更新日期：2020-07-28 00:00:00
abstract：:Intrinsically disordered proteins (IDPs) are functionally active despite lacking a well-defined three-dimensional structure. Such proteins often undergo a disorder-to-order transition, or induced folding, when binding to their specific physiological partner. Because of cooperativity, the folding and binding steps typi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.7b00350
更新日期：2017-07-25 00:00:00
abstract：:Protein folding in vivo takes place in a highly crowded environment. The resulting excluded volume forces are thought to stabilize folded forms of proteins. In agreement, many in vitro studies have shown that the presence of macromolecular crowding agents increases the stability of folded proteins but often by only a ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi500222g
更新日期：2014-04-15 00:00:00
abstract：:Isopentenyl phosphate kinase (IPK) catalyzes the phosphorylation of isopentenyl phosphate to form the isoprenoid precursor isopentenyl diphosphate in the archaeal mevalonate pathway. This enzyme is highly homologous to fosfomycin kinase (FomA), an antibiotic resistance enzyme found in a few strains of Streptomyces and...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi201662k
更新日期：2012-01-31 00:00:00
abstract：:Memapsin 2 (beta-secretase) is the membrane-anchored aspartic protease that initiates the cleavage of beta-amyloid precursor protein (APP), leading to the production of amyloid-beta (Abeta), a major factor in the pathogenesis of Alzheimer's disease. The active site of memapsin 2 has been shown, with kinetic data and c...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi048106k
更新日期：2005-01-11 00:00:00
abstract：:Drug intervention that prevents reabsorption of circulating bile acids by the apical (ileal) sodium/bile acid cotransporter (ASBT) may be a promising new therapy for lowering of plasma cholesterol. 2164U90 is a benzothiazepine-based competitive inhibitor of bile acid transport with K(i) values of approximately 10 and ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0205404
更新日期：2002-12-17 00:00:00
abstract：:Caldesmon from chicken gizzard muscle has been examined for its ability to interact with caltropin using affinity chromatography and the fluorescent probe acrylodan. The action of caltropin on the inhibitory effect of caldesmon on actomyosin ATPase was also studied. Like calmodulin, caltropin could release the inhibit...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00162a031
更新日期：1992-12-01 00:00:00
abstract：:1-Bromovinyl (I), Z-2-bromovinyl (II), 1,2-dibromoethyl (III), and a series of 4-(halomethyl)-2-nitrophenyl (IVa-c) diethyl phosphate esters were examined as substrates and mechanism-based inhibitors for the bacterial phosphotriesterase. All of these compounds were found to act as substrates for the enzyme. Inhibitor ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi970680r
更新日期：1997-07-22 00:00:00
abstract：:Two transcription factors, CRP and CytR, mediate positive and negative control of nine cistrons involved in nucleoside catabolism and recycling in Escherichia coli. The ability of multiple transcription factors to combine in different ways to confer differential gene regulation is of significant interest in both proka...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi901583n
更新日期：2010-01-26 00:00:00
abstract：:Many strains of Campylobacter jejuni display modified heptose residues in their capsular polysaccharides (CPS). The precursor heptose was previously shown to be GDP-d-glycero-α-d-manno-heptose, from which a variety of modifications of the sugar moiety have been observed. These modifications include the generation of 6...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.0c00096
更新日期：2020-04-07 00:00:00
abstract：:To elucidate the mechanism of solute diffusion through lipid bilayer membranes, nearly 4 ns of molecular dynamics simulations of solutes in phospholipid bilayers was conducted. The study, the first atomic level study of solute diffusion in a lipid bilayer, involved four simulations of an all-atom representation of a f...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00210a010
更新日期：1993-11-30 00:00:00
abstract：:To study fibronectin (FN) conformation and assembly, we generated several deletion mutants: FNΔI1-5, FNΔIII1-3, FNΔIII4-8, and FNΔIII11-14. A monomeric form, FNmono, which lacked the C-terminal dimerization region, was also created. FNtnA-D was generated by swapping FNIII domains 1-8 in FNΔIII11-14 with seven FNIII do...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.7b00589
更新日期：2017-08-29 00:00:00
abstract：:To better elucidate RNA structure-function relationships and to improve the design of pharmaceutical agents that target specific RNA motifs, an understanding of RNA primary, secondary, and tertiary structure is necessary. The prediction of RNA secondary structure from sequence is an intermediate step in predicting RNA...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi3001227
更新日期：2012-07-03 00:00:00
abstract：:Traditionally, assigning the heme protein resonances has relied heavily on the comparison of spectra arising from protein reconstituted with specifically deuterated hemes and the native form. Such an approach can identify tentatively the broad, overlapping signals in the Fe(II) high-spin heme protein spectra. Although...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00202a012
更新日期：1994-09-13 00:00:00
abstract：:We have used nucleobase substitution and kinetic analysis to test the hypothesis that hammerhead catalysis occurs by a general acid-base mechanism, in which nucleobases are directly involved in deprotonation of the attacking 2'-hydroxyl group and protonation of the 5'-oxygen that serves as the leaving group in the cle...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi047941z
更新日期：2005-05-31 00:00:00
abstract：:Each homologous lobe of human serum transferrin (hTF) has one Fe(3+) ion bound by an aspartic acid, a histidine, two tyrosine residues, and two oxygens from the synergistic anion, carbonate. Extensive characterization of these ligands in the N-terminal lobe has been carried out. Despite sharing the same set of ligands...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi050015f
更新日期：2005-06-07 00:00:00
abstract：:A pathogenic bacterium has its own mechanisms for not only pathogenic attack but also exogenous invasion defense, in which the bacterial cell wall is the front line of attack and defense. We developed a biochemical lanthanide-encoding approach to quantify the uncanonical d-amino acid (d-X) that was edited in a small p...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.0c00614
更新日期：2020-09-29 00:00:00
abstract：:Urea lesions are formed in DNA because of free radical damage of the thymine base, and their occurrence in DNA blocks DNA polymerases, which has deleterious consequences. Recently, it has been shown that urea is capable of forming hydrogen bonding and stacking interactions with nucleobases, which are responsible for t...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.6b00309
更新日期：2016-10-11 00:00:00
abstract：:Hydrogen exchange of the individual amide protons of alanine-90 (F5), glutamine-91 (F6), serine-92 (F7), and histidine-93 (F8) residues in cyanometmyoglobin of sperm whale has been studied by 1H nuclear magnetic resonance spectroscopy at 360 MHz. The amide proton resonance of F5, F6, and F7 have been assigned by use o...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00347a024
更新日期：1985-12-17 00:00:00
abstract：:The ligand-binding dynamics and the reaction with O(2) of the fully (five-electron) reduced cytochrome caa(3) from the thermohalophilic bacterium Rhodothermus (R.) marinus were investigated. The enzyme is a proton pump which has all the residues of the proton-transfer pathways found in the mitochondrial-like enzymes c...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi010344h
更新日期：2001-09-04 00:00:00
abstract：:The minimum oligosaccharide structure required for binding to the potent HIV-inactivating protein cyanovirin-N (CV-N) was determined by saturation-transfer difference (STD) NMR spectroscopy. Despite the low molecular mass of the protein (11 kDa), STD-NMR spectroscopy allowed the precise atomic mapping of the interacti...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi048676k
更新日期：2004-11-09 00:00:00
abstract：:The LAGLIDADG homing endonucleases include free-standing homodimers, pseudosymmetric monomers, and related enzyme domains embedded within inteins. DNA-bound structures of homodimeric I-CreI and monomeric I-SceI indicate that three catalytic divalent metal ions are distributed across a pair of overlapping active sites,...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi048970c
更新日期：2004-11-09 00:00:00
abstract：:Small molecule allostery modifies protein function but is not easily discovered. We introduce mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), a method for identifying physiologically relevant, low-affinity metabolite-protein interactions using unmodified pr...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi201313s
更新日期：2012-01-10 00:00:00
abstract：:The present study focuses on ligand-protein interactions in a rhodopsin analogue generated from bovine opsin and the 10-methyl homologue of 11-cis-retinal. The analogue pigment displays a reduced alpha-band at 506 +/- 2 and a stronger beta-band at 325 nm. Remarkably, the rotational strength of these bands observed in ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi972397y
更新日期：1998-02-03 00:00:00
abstract：:The effect of myosin on the structure of two sequences on G-actin, a loop between residues 39 and 52 and a segment between residues 61 and 69 from the NH2-terminus, was probed by limited proteolytic digestions of G-actin in the presence of the myosin subfragment 1 isozyme S-1(A2). Under the experimental conditions of ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00126a014
更新日期：1992-03-24 00:00:00
abstract：:Electron donation from the soluble cytochrome (cyt) c2 to the photooxidized primary donor, P+, of reaction centers isolated from Rhodobacter sphaeroides was studied by using chemical zero-length cross-linking. This cross-linking stabilizes a 1:1 covalent complex between subunit M of the reaction center and cyt c2. In ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi961350u
更新日期：1997-02-11 00:00:00
abstract：:A Ca(2+)-activated thiol protease was purified from Drosophila melanogaster. The procedure involves Phenyl-Sepharose, Reactive Red-Agarose and Q-Sepharose fast flow (or MonoQ) chromatographic steps. The enzyme eluting from Q-Sepharose fast flow seems to be homogeneous as judged by silver staining on SDS-PAGE: it consi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00150a012
更新日期：1992-09-08 00:00:00
