Abstract:
:In this work we modeled the circular dichroism (CD) spectrum of LHCII, the main light harvesting antenna of photosystem II of higher plants. Excitonic calculations are performed for a monomeric subunit, taken from the crystal structure of trimeric LHCII from spinach [Liu, Z. F., Yan, H. C., Wang, K. B., Kuang, T. Y., Zhang, J. P., Gui, L. L., An, X. M., and Chang, W. R. (2004) Nature 428, 287-292]. All of the major features of the CD spectrum above 450 nm are satisfactorily reproduced, and possible orientations of the Chl and carotenoid transition dipole moments are identified. The obtained modeling parameters are used to simulate the CD spectra of two complexes with altered pigment composition: a mutant lacking Chls a 611-612 and a complex lacking the carotenoid neoxanthin. By removing the relevant pigment(s) from the structure, we are able to reproduce their spectra, which implies that the alteration does not disturb the overall structure. The CD spectrum of trimeric LHCII shows a reversed relative intensity of the two negative bands around 470 and 490 nm as compared to monomeric LHCII. The simulations reproduce this reversal, indicating that it is mainly due to interactions between chromophores in different monomeric subunits, and the trimerization does not induce observable changes in the monomeric structure. Our simulated spectrum resembles one of two different trimeric CD spectra reported in literature. We argue that the differences in the experimental trimeric CD spectra are caused by changes in the strength of the monomer-monomer interactions due to the differences in detergents used for the purification of the complexes.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Georgakopoulou S,van der Zwan G,Bassi R,van Grondelle R,van Amerongen H,Croce Rdoi
10.1021/bi062031ysubject
Has Abstractpub_date
2007-04-24 00:00:00pages
4745-54issue
16eissn
0006-2960issn
1520-4995journal_volume
46pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::The continued rise of antibiotic-resistant infections coupled with the limited pipeline of new antimicrobials highlights the pressing need for the development of new antibacterial agents. One potential pathway for new agents is de novo purine biosynthesis as studies have shown that bacteria and lower eukaryotes synthe...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.8b00939
更新日期:2019-04-30 00:00:00
abstract::The operator-binding domain of phage lambda repressor provides a model for DNA recognition by the helix-turn-helix (HTH) motif. In the wild-type protein, dimerization is mediated by hydrophobic packing (of the dyad-related helix 5), which serves as an indirect determinant of operator affinity. The mutant repressor, Ty...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00232a003
更新日期:1991-05-07 00:00:00
abstract::Cooperative binding of the bacteriophage lambda cI repressor dimer to specific sites of the phage operators OR and OL controls the developmental state of the phage. Cooperativity has long been thought to be mediated by self-assembly of repressor dimers to form tetramers which can bind simultaneously to adjacent operat...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi971368k
更新日期:1997-10-21 00:00:00
abstract::The members of the ets gene family of transcription factors are characterized by a conserved 85-residue DNA-binding region, termed the ETS domain, that lacks sequence homology to structurally characterized DNA-binding motifs. The secondary structure of the ETS domain of murine Ets-1 was determined on the basis of NMR ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00250a001
更新日期:1994-11-22 00:00:00
abstract::Because oxygen and selenium are in the same group (Family VI) in the periodic table, the site-specific mutagenesis at the atomic level by replacing RNA oxygen with selenium can provide insights on the structure and function of catalytic RNAs. We report here the first Se-derivatized ribozymes transcribed with all nucle...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi060455m
更新日期:2006-07-25 00:00:00
abstract::We have covalently attached an electron paramagnetic resonance (EPR) spin probe to Cys-670 of the motor domain of ncd (nonclaret disjunctional protein) in order to investigate conformational changes associated with the chemomechanical cycle. Spin-labeling is highly specific and does not affect ncd function as monitore...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9706881
更新日期:1997-08-12 00:00:00
abstract::Ribonuclease P2 from the thermophilic archaebacterium Sulfolobus solfataricus is a small protein (7 kDa) with a known three-dimensional structure. Inspection of the structure and molecular dynamics simulation reveal that three aromatic residues (Phe5, Phe31, and Tyr33) from the hydrophobic core have a strong van der W...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi970467v
更新日期:1997-07-22 00:00:00
abstract::The regiospecificity and stereospecificity of proton transfer in the yeast inorganic pyrophosphatase (PPase) catalyzed hydrolysis of P1,P2-bidentate Mg(H2O)4(PPi)2- were probed with exchange-inert metal complexes of imidodiphosphate (PNP) and thiopyrophosphate (PPS). PPase was unable to catalyze the hydrolysis of Mg(H...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00364a035
更新日期:1986-08-12 00:00:00
abstract::Yeast mitochondrial NAD+-specific isocitrate dehydrogenase (IDH) has previously been shown to bind specifically to 5'-untranslated regions of yeast mitochondrial mRNAs, and transcripts containing these regions have been found to allosterically inhibit activity of the enzyme. This inhibition is relieved by AMP, an allo...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0200662
更新日期:2002-06-04 00:00:00
abstract::The mechanism by which the heme-containing peroxidase, chloroperoxidase, is able to chlorinate substrates is poorly understood. One approach to advance our understanding of the mechanism of the enzyme is to determine those factors which contribute to its stability. In particular, under alkaline conditions, chloroperox...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi961512m
更新日期:1996-11-19 00:00:00
abstract::We have examined the reduction of cyanide by using the purified component proteins of nitrogenase (Av1 and Av2). The previously reported self-inhibition phenomenon was found to be an artifact. One of the two species present in cyanide solutions, CN-, was shown to be a potent reversible inhibitor (Ki = 27 microM) of to...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00261a031
更新日期:1982-08-31 00:00:00
abstract::Chemoenzymatic glycan remodeling by endoglycosidase-catalyzed deglycosylation and reglycosylation is emerging as an attractive approach for producing homogeneous glycoforms of antibodies, and the success of this approach depends on the discovery of efficient endoglycosidases and their glycosynthase mutants. We report ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.8b00719
更新日期:2018-09-04 00:00:00
abstract::The search for a rational method of developing an antimalarial vaccine (malaria caused by Plasmodium falciparum) consists of blocking receptor-ligand interaction. Conserved peptides derived from proteins involved in invasion and having strong red blood cell binding ability have thus been identified; immunization studi...
journal_title:Biochemistry
pub_type: 历史文章,杂志文章
doi:10.1021/bi050214z
更新日期:2005-05-10 00:00:00
abstract::Inflammation and subsequent cyclooxygenase-2 (COX-2) activity has long been linked with the development of cancer, although little is known about any epigenetic effects of COX-2. A product of COX-2 activation, levuglandin (LG) quickly forms covalent bonds with nearby primary amines, such as those in lysine, which lead...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi401673b
更新日期:2014-04-22 00:00:00
abstract::Cytomegaloviruses (CMVs) are ubiquitous species-specific viruses that establish acute, persistent, and latent infections. Both human and mouse CMVs encode proteins that inhibit the activation of natural killer (NK) cells by downregulating cellular ligands for the NK cell activating receptor, NKG2D. The MCMV glycoprote...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi902130j
更新日期:2010-03-23 00:00:00
abstract::Phosphoprotein particles were isolated in their native state from the physiological fluid of the estuarine clam Rangia cuneata , and the characteristics of the mineral ion-protein complex which constitutes the native particle were investigated by using mineral ion binding and mineral ion exchange techniques. The parti...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00302a017
更新日期:1984-03-27 00:00:00
abstract::The primary structure of the 43-kilodalton peripheral membrane protein (43-kDa protein) of Torpedo nicotinic postsynaptic membrane has been determined. The 43-kDa protein, which was isolated by preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis, has an amino terminus resistant to Edman degradation, ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00396a034
更新日期:1987-11-03 00:00:00
abstract::The heptadecapeptides bombolitin I and bombolitin III are two of a series of peptides postulated to be biologically active within a membrane environment. In the preceding paper [Bairaktari, E., Mierke, D.F., Mammi, S., & Peggion, E. (1990) Biochemistry (preceding paper in this issue)] the conformational preferences of...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00495a012
更新日期:1990-10-30 00:00:00
abstract::Mixed phospholipid systems of ether-linked 1,2-dihexadecylphosphatidylcholine (DHPC) and ester-linked 1,2-dipalmitoylphosphatidylcholine (DPPC) have been studied by differential scanning calorimetry and X-ray diffraction. At maximum hydration (60 wt % water), DHPC shows three reversible transitions: a main (chain melt...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00395a006
更新日期:1987-10-20 00:00:00
abstract::In the Arc repressor dimer, the side chains of Ile37 and Val41 in alpha-helix B pack against each other and against the symmetry-related side chains of Ile37' and Val41' in alpha-helix B' to form part of the hydrophobic core and the dimer interface. Following combinatorial mutagenesis of these positions, only the wild...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00010a025
更新日期:1995-03-14 00:00:00
abstract::Pineapple stem bromelain was photooxidized in the presence of Methylene Blue used as a sensitizer. The essential sulfhydryl group of the enzyme protein rapidly became inaccessible to react with 5,5'-dithiobis(nitrobenzoic acid), but the reactivity was readily regained to the original level upon treatment with dithioth...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00673a009
更新日期:1975-01-28 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::HbPresbyterian (beta 108Asn --> Lys, HbP) contains an additional positive charge (per alpha beta dimer) in the middle of the central cavity and exhibits a lower oxygen affinity than wild-type HbA in the presence of chloride. However, very little is known about the molecular origins of its altered functional properties...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9827464
更新日期:1999-08-31 00:00:00
abstract::Bax protein plays a key role in mitochondrial membrane permeabilization and cytochrome c release upon apoptosis. Our recent data have indicated that the 20-residue C-terminal peptide of Bax (BaxC-KK; VTIFVAGVLTASLTIWKKMG), when expressed intracellularly, translocates to the mitochondria and exerts lethal effect on can...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi301195f
更新日期:2012-11-20 00:00:00
abstract::The velocity of the oxidative renaturation of reduced ribonuclease A catalyzed by protein disulfide isomerase (PDI) is strongly dependent on the composition of a glutathione/glutathione disulfide redox buffer. As with the uncatalyzed, glutathione-mediated oxidative folding of ribonuclease, the steady-state velocity of...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00217a004
更新日期:1991-01-22 00:00:00
abstract::SH2 domains are protein modules which interact with specific tyrosine phosphorylated sequences in target proteins. The SH2 domain of the Src kinase binds with high affinity to a tyrosine phosphorylated peptide containing the amino acids Glu, Glu, and Ile (EEI) at the positions +1, +2, and +3 C-terminal to the phosphot...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi982974y
更新日期:1999-04-20 00:00:00
abstract::Escherichia coli DNA photolyase mediates photorepair of pyrimidine dimers occurring in UV-damaged DNA. The enzyme contains two chromophores, 1,5-dihydroflavin adenine dinucleotide (FADH2) and 5,10-methenyltetrahydrofolylpolyglutamate (MTHF). To define the roles of the two chromophores in the photochemical reaction(s) ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00485a021
更新日期:1990-08-21 00:00:00
abstract::The targeting of the insulin-responsive glucose transporter, GLUT-4, to an intracellular compartment in adipocytes and muscle is one of the key features responsible for the unique insulin sensitivity of this transporter. Through expression of epitope-tagged GLUT-4 mutants in 3T3-L1 adipocytes, two motifs have been ide...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi980988y
更新日期:1999-02-02 00:00:00
abstract::1H NMR spectral editing techniques can select the distinct signals of lactate, pyruvate, beta-hydroxybutyrate, and acetoacetate and provide a unique way to monitor the biochemical processes in vivo. These metabolite levels reflect the near-equilibrium dehydrogenase activity and therefore the cellular redox state. The ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00160a029
更新日期:1992-11-17 00:00:00
abstract::The Bacillus subtilis DNA-dependent RNA polymerase holoenzyme and core enzyme each contain approximately two atoms of zinc per molecule. When the dissociated subunits of the enzyme are passed through a blue dextran-Sepharose affinity column, only the beta subunit binds to the column. The total zinc content of the enzy...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00632a012
更新日期:1977-06-28 00:00:00