Nuclear magnetic resonance study of the Schiff base in bacteriorhodopsin: counterion effects on the 15N shift anisotropy.

Abstract:

:High-resolution, solid-state 15N NMR has been used to study the chemical shift anisotropies of the Schiff bases in bacteriorhodopsin (bR) and in an extensive series of model compounds. Using slow-spinning techniques, we are able to obtain sufficient rotational sideband intensity to determine the full 15N chemical shift anisotropy for the Schiff base nitrogen in bR548 and bR568. Comparisons are made between all-trans-bR568 and N-all-trans-retinylidene butylimine salts with halide, phenolate, and carboxylate counterions. It is argued that for the model compounds the variation in 15N chemical shift reflects the variation in (hydrogen) bond strength with the various counterions. The results suggest that carboxylates and tyrosinates may form hydrogen bonds of comparable strength in a hydrophobic environment. Thus, the hydrogen bonding strength of a counterion depends on factors that are not completely reflected in the solution pKa of its conjugate acid. For the model compounds, the two most downfield principal values of the 15N chemical shift tensor, sigma 22 and sigma 33, vary dramatically with different counterions, whereas sigma 11 remains essentially unaffected. In addition, there exists a linear correlation between sigma 22 and sigma 33, which suggests that a single mechanism is responsible for the variation in chemical shifts present in all three classes of model compounds. The data for bR568 follow this trend, but the isotropic shift is 11 ppm further upfield than any of the model compounds. This extreme value suggests an unusually weak hydrogen bond in the protein.

journal_name

Biochemistry

journal_title

Biochemistry

authors

de Groot HJ,Harbison GS,Herzfeld J,Griffin RG

doi

10.1021/bi00434a033

subject

Has Abstract

pub_date

1989-04-18 00:00:00

pages

3346-53

issue

8

eissn

0006-2960

issn

1520-4995

journal_volume

28

pub_type

杂志文章
  • Molecular exchange at the lipid-rhodopsin interface: spin-label electron spin resonance studies of rhodopsin-dimyristoylphosphatidylcholine recombinants.

    abstract::The photoreceptor protein rhodopsin has been reconstituted with a single phospholipid species, dimyristoylphosphatidylcholine, at a range of different lipid/protein ratios, and the exchange rate at the lipid-protein interface has been determined from the electron spin resonance spectra of spin-labeled phosphatidylchol...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00385a045

    authors: Ryba NJ,Horváth LI,Watts A,Marsh D

    更新日期:1987-06-02 00:00:00

  • Some effects of ionophore A23187 on energy utilization and the distribution of cations and anions in mitochondria.

    abstract::The effects of ionophore A23187 on the movements of Ca2+, Mg2+, H+ phosphate, and succinate and its effects on energy utilization by mitochondria have been studied as a function of ionophore concentrations. At a low ratio of the compound to mitochondrial protein, below that required for maximal uncoupling, an apparent...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00657a032

    authors: Pfeiffer DR,Hutson SM,Kauffman RF,Lardy HA

    更新日期:1976-06-15 00:00:00

  • Effects of peptide length and composition on binding to an empty class I MHC heterodimer.

    abstract::Class I major histocompatibility complex (MHC) proteins present peptide antigens to T cells during the immune response against viruses. Peptides are loaded into newly synthesized class I heterodimers in the endoplasmic reticulum such that most or all cell surface class I molecules contain peptides derived from endogen...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00192a020

    authors: Fahnestock ML,Johnson JL,Feldman RM,Tsomides TJ,Mayer J,Narhi LO,Bjorkman PJ

    更新日期:1994-07-05 00:00:00

  • Impact of Rett Syndrome Mutations on MeCP2 MBD Stability.

    abstract::Rett syndrome causing missense mutations in the methyl-CpG-binding domain (MBD) of methyl CpG-binding protein 2 (MeCP2) were investigated both in silico and in vitro to reveal their effect on protein stability. It is demonstrated that the vast majority of frequently occurring mutations in the human population indeed a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00790

    authors: Kucukkal TG,Yang Y,Uvarov O,Cao W,Alexov E

    更新日期:2015-10-20 00:00:00

  • Poly(pro)II helices in globular proteins: identification and circular dichroic analysis.

    abstract::A method to identify poly(L-proline)-type (PII) conformation in crystal structures of globular proteins is presented. Short segments of PII structure were identified in globular protein structures, and these form a significant fraction of the residues which are not assigned to alpha-helix, beta-sheet, and beta-turns. ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00199a028

    authors: Sreerama N,Woody RW

    更新日期:1994-08-23 00:00:00

  • Kinetic mechanisms of polyphosphate glucokinase from Mycobacterium tuberculosis.

    abstract::Polyphosphate glucokinase from Mycobacterium tuberculosis catalyzes the phosphorylation of glucose using inorganic polyphosphates [poly(P)] or ATP. The steady-state kinetic mechanisms of the poly(P)- and ATP-dependent glucokinase reactions were investigated using initial velocity, product inhibition, and dead-end inhi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9528659

    authors: Hsieh PC,Kowalczyk TH,Phillips NF

    更新日期:1996-07-30 00:00:00

  • Characterization and stereochemistry of cofactor oxidation by a type II dihydrofolate reductase.

    abstract::Type II dihydrofolate reductases (DHFRs) encoded by the R67 and R388 plasmids are different both in sequence and in structure from known chromosomal DHFRs. These plasmid-derived DHFRs are responsible for conferring trimethoprim resistance to the host strain. A derivative of R388 DHFR, RBG200, has been cloned and overp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00494a011

    authors: Brito RM,Reddick R,Bennett GN,Rudolph FB,Rosevear PR

    更新日期:1990-10-23 00:00:00

  • Kinetics of binding of oligosaccharides to a homogeneous pneumococcal antibody: dependence on antigen chain length suggests a labile intermediate complex.

    abstract::Temperature-jump experiments were performed with di-, tetra-, and hexasaccharides derived from type III pneumococcal polysaccharide using a homogeneous corresponding antibody IgG 45-394. A decrease in stability of the oligosaccharide-antibody complexes with decreasing chain length was observed and entirely reflected i...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00637a023

    authors: Maeda H,Schmidt-Kessen A,Engel J,Jaton JC

    更新日期:1977-09-06 00:00:00

  • Formation of radiation-induced cross-links between thymine and tyrosine: possible model for cross-linking of DNA and proteins by ionizing radiation.

    abstract::A model for radiation-induced cross-linking of DNA and proteins has been developed. It is based on initial formation of free radicals on a DNA base, i.e., thymine, and on an amino acid, i.e., tyrosine. It was demonstrated that interaction of these radicals is highly favored as measured by their kinetics and the cross-...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00322a034

    authors: Simic MG,Dizdaroglu M

    更新日期:1985-01-01 00:00:00

  • Modified bases in RNA reduce secondary structure and enhance hybridization.

    abstract::Secondary structure in RNA targets is a significant barrier to short DNA probes. However, when such targets are the end product of an in vitro amplification scheme, it is possible to carry out transcription in the presence of nucleoside triphosphate analogues that reduce secondary structure of the RNA without impairin...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049196w

    authors: Gamper HB Jr,Gewirtz A,Edwards J,Hou YM

    更新日期:2004-08-10 00:00:00

  • Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration.

    abstract::The data and approach reported in paper I (Hanlon et al., 1975, preceding paper) have been used to calculate the fractional changes in secondary structure of calf thymus deoxyribonucleic acid which occur in aqueous solutions as a function of the concentration of NaCl, KCl, LiCl, CsCl, and NH4Cl. There is a continuous ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00679a018

    authors: Wolf B,Hanlon S

    更新日期:1975-04-22 00:00:00

  • Chimeric human calcitonin and glucagon receptors reveal two dissociable calcitonin interaction sites.

    abstract::Two chimeric receptors were constructed by transposing the coding regions for the putative N-terminal domains of the human calcitonin (hCTR) and glucagon (hGGR) receptors. These receptors were stably expressed as glycosylated proteins with molecular masses of 80 kDa for the calcitonin receptor N-terminus chimera (NtCT...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00003a040

    authors: Stroop SD,Kuestner RE,Serwold TF,Chen L,Moore EE

    更新日期:1995-01-24 00:00:00

  • Ivermectin and nodulisporic acid receptors in Drosophila melanogaster contain both gamma-aminobutyric acid-gated Rdl and glutamate-gated GluCl alpha chloride channel subunits.

    abstract::35S-labeled derivatives of the insecticides nodulisporic acid and ivermectin were synthesized and demonstrated to bind with high affinity to a population of receptors in Drosophila head membranes that were previously shown to be associated with a glutamate-gated chloride channel. Nodulisporic acid binding was modeled ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi015920o

    authors: Ludmerer SW,Warren VA,Williams BS,Zheng Y,Hunt DC,Ayer MB,Wallace MA,Chaudhary AG,Egan MA,Meinke PT,Dean DC,Garcia ML,Cully DF,Smith MM

    更新日期:2002-05-21 00:00:00

  • Inhibition of islet amyloid polypeptide fibril formation: a potential role for heteroaromatic interactions.

    abstract::The formation of amyloid fibril is associated with major human diseases, including Alzheimer's disease, prion diseases, and type 2 diabetes. Methods for efficient inhibition of amyloid fibril formation are therefore highly clinically important. A principal approach for the inhibition of amyloid formation is based on t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi048582a

    authors: Porat Y,Mazor Y,Efrat S,Gazit E

    更新日期:2004-11-16 00:00:00

  • Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions.

    abstract::The C2A domain of synaptotagmin 7 (Syt7) is a Ca(2+) and membrane binding module that docks and inserts into cellular membranes in response to elevated intracellular Ca(2+) concentrations. Like other C2 domains, Syt7 C2A binds Ca(2+) and membranes primarily through three loop regions; however, it docks at Ca(2+) conce...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00422

    authors: Chon NL,Osterberg JR,Henderson J,Khan HM,Reuter N,Knight JD,Lin H

    更新日期:2015-09-22 00:00:00

  • The ice-binding site of sea raven antifreeze protein is distinct from the carbohydrate-binding site of the homologous C-type lectin.

    abstract::Antifreeze proteins lower the freezing point of their solution by binding to ice and inhibiting its growth. One of several structurally different antifreeze proteins in fishes (type II) is homologous to the carbohydrate-recognition domain of Ca2+-dependent lectins and adopts the same three-dimensional fold. Type II an...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9820513

    authors: Loewen MC,Gronwald W,Sönnichsen FD,Sykes BD,Davies PL

    更新日期:1998-12-22 00:00:00

  • 2D NMR studies and 3D structure of the parallel-stranded duplex oligonucleotide Acrm5-alpha-d(TCTAAACTC)-beta-d(AGATTTGAG) via complete relaxation matrix analysis of the NOE effects and molecular mechanics calculations.

    abstract::The three-dimensional structure of the duplex formed by the association of the unnatural oligonucleotide alpha-d(TCTAAACTC) covalently linked to an acridine derivative (m5Acr) with its natural and parallel complementary sequence beta-d(AGATTTGAG) was investigated by nuclear magnetic resonance spectroscopy and constrai...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00472a031

    authors: Guesnet JL,Vovelle F,Thuong NT,Lancelot G

    更新日期:1990-05-22 00:00:00

  • Structural, Functional, and Dynamical Responses of a Protein in a Restricted Environment Imposed by Macromolecular Crowding.

    abstract::The intercellular environment is known to be very different from the environment where most of the elementary biological processes are studied in the laboratory. As a result, there was a considerable effort on cell mimicking either by confinement or by introducing macromolecular crowding. In the present study, dextran...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b00599

    authors: Das N,Sen P

    更新日期:2018-10-23 00:00:00

  • The adhesive specificity of the soluble human lectin, IgE-binding protein, toward lipid-linked oligosaccharides. Presence of the blood group A, B, B-like, and H monosaccharides confers a binding activity to tetrasaccharide (lacto-N-tetraose and lacto-N-ne

    abstract::The immunoglobulin E-binding protein, epsilon BP (also known as CBP35, Mac-2, L-34, and L-29), is a beta-galactoside-binding protein of approximately 30 kDa and a member of the animal lectin family termed S-type or S-Lac. Multiple biological activities have been attributed to this lectin such as mediation of IgE bindi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00186a038

    authors: Feizi T,Solomon JC,Yuen CT,Jeng KC,Frigeri LG,Hsu DK,Liu FT

    更新日期:1994-05-24 00:00:00

  • Structure of a hydroxyl radical induced DNA-protein cross-link involving thymine and tyrosine in nucleohistone.

    abstract::Hydroxyl radical induced formation of a DNA-protein cross-link involving thymine and tyrosine in nucleohistone is described. Hydroxyl radicals were generated in N2O-saturated aqueous solution by ionizing radiation. Samples of nucleohistone were hydrolyzed with HCl and trimethylsilylated. Analysis of irradiated samples...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00434a071

    authors: Dizdaroglu M,Gajewski E,Reddy P,Margolis SA

    更新日期:1989-04-18 00:00:00

  • Structures of the modified folates in the thermophilic archaebacteria Pyrococcus furiosus.

    abstract::The structures of the modified folates present in Pyrococcus furiosus have been determined. This was accomplished largely by the characterization of the arylamines resulting from the air oxidative cleavage of the reduced modified folates present in these cells, using both chemical and enzymatic methods. Cell extracts ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00054a003

    authors: White RH

    更新日期:1993-01-26 00:00:00

  • Sequences of B-chain/domain 1-10/1-9 of insulin and insulin-like growth factor 1 determine their different folding behavior.

    abstract::Although insulin and insulin-like growth factor-1 (IGF-1) belong to one family, insulin folds into one thermodynamically stable structure, while IGF-1-folds into two thermodynamically stable structures (native and swap forms). We have demonstrated previously that the bifurcating folding behavior of IGF-1 is mainly con...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049710y

    authors: Chen Y,You Y,Jin R,Guo ZY,Feng YM

    更新日期:2004-07-20 00:00:00

  • Detection of RNA-Protein Interactions in Living Cells with SHAPE.

    abstract::SHAPE-MaP is unique among RNA structure probing strategies in that it both measures flexibility at single-nucleotide resolution and quantifies the uncertainties in these measurements. We report a straightforward analytical framework that incorporates these uncertainties to allow detection of RNA structural differences...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00977

    authors: Smola MJ,Calabrese JM,Weeks KM

    更新日期:2015-11-24 00:00:00

  • 1H NMR assignment and global fold of napin BnIb, a representative 2S albumin seed protein.

    abstract::Napin BnIb is a representative member of the 2S albumin seed proteins, which consists of two polypeptide chains of 3.8 and 8.4 kDa linked by two disulfide bridges. In this work, a complete assignment of the 1H spectra of napin BnIb has been carried out by two-dimensional NMR sequence-specific methods and its secondary...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi961748q

    authors: Rico M,Bruix M,González C,Monsalve RI,Rodríguez R

    更新日期:1996-12-10 00:00:00

  • Direct NMR evidence that prolidase is specific for the trans isomer of imidodipeptide substrates.

    abstract::The in vitro hydrolysis by porcine kidney prolidase of the imidodipeptide L-alanyl-L-proline was monitored by using 1H high-resolution NMR spectroscopy. The dipeptide exists as an equilibrium mixture of isomers with cis or trans conformation about the peptide bond. The 13C and 1H NMR spectra of the dipeptide displayed...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00353a016

    authors: King GF,Middlehurst CR,Kuchel PW

    更新日期:1986-03-11 00:00:00

  • Exploring the binding site of delta(lac)-acetogenin in bovine heart mitochondrial NADH-ubiquinone oxidoreductase.

    abstract::Biochemical characterization of the inhibition mechanism of Deltalac-acetogenins synthesized in our laboratory indicated that they are a new type of inhibitor of bovine heart mitochondrial NADH-ubiquinone oxidoreductase (complex I) [Murai, M., et al. (2006) Biochemistry 45, 9778-9787]. To identify the binding site of ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi100454b

    authors: Kakutani N,Murai M,Sakiyama N,Miyoshi H

    更新日期:2010-06-15 00:00:00

  • Overexpression and functional characterization of the extracellular domain of the human alpha1 glycine receptor.

    abstract::A novel truncated form (residues 1-214, with a randomized C-terminal tail) of the ligand-binding extracellular domain (ECD) of the human alpha1 glycine receptor (GlyR), with amino acids from the corresponding sequence of an acetylcholine binding protein (AChBP) substituted for two relatively hydrophobic membrane-proxi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi800659x

    authors: Liu Z,Ramanoudjame G,Liu D,Fox RO,Jayaraman V,Kurnikova M,Cascio M

    更新日期:2008-09-16 00:00:00

  • Interaction of lipoprotein lipase with phospholipid vesicles: effect on protein and lipid structure.

    abstract::The interaction of lipoprotein lipase (LpL) and a nonhydrolyzable phosphatidylcholine, 1,2-ditetradecyl-rac-glycero-3-phosphocholine (C14-ether-PC), has been studied by several physical methods. Analysis of the circular dichroic spectrum of LpL gave the following fractional conformation: 35% alpha-helix, 30% beta-plea...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00352a020

    authors: McLean LR,Larsen WJ,Jackson RL

    更新日期:1986-02-25 00:00:00

  • Interactions of the antimicrobial peptides temporins with model biomembranes. Comparison of temporins B and L.

    abstract::Temporins are short (10-13 amino acids) and linear antimicrobial peptides first isolated from the skin of the European red frog, Rana temporaria, and are effective against Gram-positive bacteria and Candida albicans. To get insight into their mechanism(s) of action, we compared the effects on model membranes exerted b...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi011929e

    authors: Zhao H,Rinaldi AC,Di Giulio A,Simmaco M,Kinnunen PK

    更新日期:2002-04-02 00:00:00

  • Interaction between Cellobiose Dehydrogenase and Lytic Polysaccharide Monooxygenase.

    abstract::Lytic polysaccharide monooxygenases (LPMOs) are ubiquitous oxidoreductases, facilitating the degradation of polymeric carbohydrates in biomass. Cellobiose dehydrogenase (CDH) is a biologically relevant electron donor in this process, with the electrons resulting from cellobiose oxidation being shuttled from the CDH de...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b01178

    authors: Laurent CVFP,Breslmayr E,Tunega D,Ludwig R,Oostenbrink C

    更新日期:2019-03-05 00:00:00