Abstract:
:ZFY, a male-associated Zn-finger protein encoded by the human Y chromosome, exhibits a distinctive two-finger repeat: whereas odd-numbered domains fit a general consensus, even-numbered domains exhibit systematic differences. Do these odd and even sequences encode structurally distinct surfaces for DNA recognition? As a first step toward answering this question, we have recently described the sequential 1H NMR assignment of a representative nonconsensus Zn finger (designated ZFY-6T) based on 2D NMR studies of a 30-residue peptide [Kochoyan, M., Havel, T.F., Nguyen, D.T., Dahl, C.E., Keutmann, H. T., & Weiss, M.A. (1991) Biochemistry 30, 3371-3386]. Initial structural modeling by distance geometry/simulated annealing (DG/SA) demonstrated that this peptide retained the N-terminal beta-hairpin and C-terminal alpha-helix (beta beta alpha motif) observed in consensus Zn fingers. However, the precision of this initial structure was limited by resonance overlap, which led to ambiguities in the assignment of key NOEs in the hydrophobic core. In this paper these ambiguities are resolved by selective deuterium labeling, enabling a refined structure to be calculated by DG/SA and restrained molecular dynamics. These calculations provide a detailed view of the hydrophobic core and protein surface, which are analyzed in reference to previously characterized Zn fingers. Variant (even) and consensus (odd) aromatic residues Y10 and F12, shown in an "aromatic swap" analogue to provide equivalent contributions to the hydrophobic core [Weiss, M.A., & Keutmann, H.T. (1990) Biochemistry 29, 9808-9813], nevertheless exhibit striking differences in packing interactions: Y10--but not F12--contributes to a contiguous region of the protein surface defined by putative specificity-determining residues. Alternating surface architectures may have implications for the mechanism of DNA recognition by the ZFY two-finger repeat.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Kochoyan M,Keutmann HT,Weiss MAdoi
10.1021/bi00243a005subject
Has Abstractpub_date
1991-07-23 00:00:00pages
7063-72issue
29eissn
0006-2960issn
1520-4995journal_volume
30pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::High-resolution proton nuclear magnetic resonance (1H NMR) has been used to study the conformation and dynamics of biosynthetic analogues of actinomycin D that have been substituted at one or both of the 3'-amino acids with azetidine-2-carboxylic acid, pipecolic acid, or 4-ketoproline for one or both of the prolines. ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00540a007
更新日期:1982-05-25 00:00:00
abstract::The amino acid histidine can play a significant role in the structure and function of proteins. Its various functions include enzyme catalysis, metal binding activity, and involvement in cation-π, π-π, salt-bridge, and other types of noncovalent interactions. Although histidine's imidazole nitrogens (Nδ and Nε) are kn...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00253
更新日期:2016-07-12 00:00:00
abstract::Activation of a growth factor receptor tyrosine kinase (RTK) is accompanied by a rapid autophosphorylation of the receptor on tyrosine residues. Receptor activation has been shown to promote the association of signal-transducing proteins containing SH2 domains (second domain of src homology). These receptor-associated...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00089a028
更新日期:1993-09-28 00:00:00
abstract::The effect of hydrostatic pressure upon solutions of chymotrypsinogen and lysozyme at room temperature has been followed by employing a new technique [Chryssomallis, G. S., Drickamer, H. G., & Weber, G. (1978) J. Appl. Phys. 49, 3084] that permits the measurement of fluorescence polarization at pressures of up to 10 k...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00517a002
更新日期:1981-07-07 00:00:00
abstract::The effect of tropomyosin alone on the binding of myosin subfragment 1 (S-1) to actin was compared to that of troponin-tropomyosin, with and without Ca2+. Over a range of ionic strength and with different ligands (adenyl-5'-yl imidodiphosphate, pyrophosphate, and adenosine 5'-diphosphate), tropomyosin confers slight c...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00280a027
更新日期:1983-05-24 00:00:00
abstract::Olivopontocerebellar atrophy with retinal degeneration is a hereditary neurodegenerative disorder that belongs to the subtype II of the autosomal dominant cerebellar ataxias and is characterized by early-onset cerebellar and macular degeneration preceded by diagnostically useful tritan colorblindness. The gene mutated...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi992694y
更新日期:2000-06-13 00:00:00
abstract::Voltage-dependent L-type calcium (Ca) channels are heteromultimeric proteins that are regulated through phosphorylation by cAMP-dependent protein kinase (PKA). We demonstrated that the beta 2 subunit was a substrate for PKA in intact cardiac myocytes through back-phosphorylation experiments. In addition, a heterologou...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi990896o
更新日期:1999-08-10 00:00:00
abstract::Deuterium NMR has been used to investigate the structure and dynamic state of cytochrome c complexed with bilayers of cardiolipin. Reductive methylation was employed to prepare [N epsilon, N epsilon-C2H3]lysyl cytochrome c, and deuterium exchange provided labeling of backbone sites to give [amide-2H]cytochrome c or mo...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00230a010
更新日期:1991-04-23 00:00:00
abstract::The peptide hormone bradykinin exerts important biological functions by binding to and activating bradykinin B2 receptors. B2 receptors belong to the seven transmembrane domain (7TM) receptor family. Cloning of the cDNA sequences for the rat, human, and mouse bradykinin B2 receptor revealed several in-frame AUG triple...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9601060
更新日期:1996-06-11 00:00:00
abstract::Prothrombin is the precursor of thrombin, a central enzyme in coagulation. Autoantibodies to prothrombin are associated with thromboembolism, but the mechanisms by which the antibodies modulate the coagulation processes are not understood. We screened a panel of 34 monoclonal antibody light chains isolated from patien...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi992588w
更新日期:2000-05-30 00:00:00
abstract::A heparin-induced conformational change is required to convert antithrombin from a slow to a fast inhibitor of factor Xa. It has been proposed [van Boeckel et al. (1994) Nat. Struct. Biol. 1, 423-425] that the reactive center residue P14 is inserted into beta-sheet A in native antithrombin and is displaced from the be...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9604643
更新日期:1996-07-02 00:00:00
abstract::The bidirectional transformation of a protein between its native water-soluble and integral transmembrane conformations is demonstrated for FraC, a hemolytic protein of the family of pore-forming toxins. In the presence of biological membranes, the water-soluble conformation of FraC undergoes a remarkable structural r...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b01112
更新日期:2015-11-24 00:00:00
abstract::The second-order electron transfer reaction between cytochrome b5 and cytochrome c has been studied by cyclic voltammetry utilizing a gold electrode modified with beta-mercaptopropionate. When cyclic voltammetry is performed on a solution containing a mixture of cytochrome b5, cytochrome c and polylysine, cytochrome b...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9529723
更新日期:1996-09-24 00:00:00
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
更新日期:2008-09-16 00:00:00
abstract::Sensory rhodopsin I (SRI) is a seven-transmembrane helix retinylidene protein that mediates color-sensitive phototaxis responses through its bound transducer HtrI in the archaeon Halobacterium salinarum. Deprotonation of the Schiff base attachment site of the chromophore accompanies formation of the SRI signaling stat...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi991180w
更新日期:1999-10-05 00:00:00
abstract::The interaction of novel, tetrafunctional bisplatinum compounds with DNA was investigated. These compounds have bis(vicinal 1,2-diamines) as ligand. The reactions' efficiency, types of cross-links, alterations of the global DNA structure, and sequence selectivity differ significantly from the corresponding features of...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi970741l
更新日期:1997-09-23 00:00:00
abstract::Efforts toward the development of RNA-based drug leads have been challenging because of the complexity and dynamic nature of RNA structures as therapeutic targets. The transactivation response (TAR) RNA and cognate Tat protein of HIV have long been recognized as promising antiviral targets, and recent works have ident...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b00325
更新日期:2015-06-16 00:00:00
abstract::The fidelity of DNA strand transfer reactions catalyzed by human immunodeficiency virus type 1 reverse transcriptase has been studied in vitro. A model system involving two sequential DNA strand transfers was developed to simulate the process of forced copy-choice recombination. A propensity for nucleotide misincorpor...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00179a014
更新日期:1994-04-05 00:00:00
abstract::Suberyldicholine-induced ion translocation in the millisecond time region in acetylcholine receptor rich membrane vesicles prepared from the electric organ of Electrophorus electricus was investigated in eel Ringer's solution, pH 7.0, 1 degree C. A quench-flow technique with a time resolution of 5 ms was used to measu...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00294a041
更新日期:1983-12-06 00:00:00
abstract::A modified multiple binding equilibria treatment is presented that allows determination of thermodynamic parameters of the interaction of phospholipids with integral membrane proteins solubilized in excess detergent. Lipid binding is modeled as a series of exchange reactions between lipid molecules and detergent molec...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00376a019
更新日期:1987-01-27 00:00:00
abstract::Proton NMR studies were conducted on the complementary 15-mer duplex d(5'-TACTCTTCTTGACCT).(5'-AGGTCAAGAAGAGTA) (designated as unmodified 15-mer duplex) spanning a portion of the mouse c-Ha-ras protooncogene centered around codon 61. Identical studies were carried out on the same sequence, after specific modification ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00155a011
更新日期:1992-10-13 00:00:00
abstract::The positions, with respect to the plasma membrane, of lysine 905, contained in the peptide QRKIVE, and of lysine 1012, contained in the carboxy-terminal peptide, RPGGWVEKETYY, of ovine Na+/K(+)-transporting ATPase have been reported to be cytoplasmic and extracytoplasmic, respectively [Bayer, R. (1990) Biochemistry 2...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00062a012
更新日期:1993-03-23 00:00:00
abstract::The structure of the subgel phase of dipalmitoylphosphatidylglycerol (DPPG) has been analyzed by X-ray diffraction techniques. Diffraction recorded from highly oriented DPPG specimens in the subgel phase extends to 2-A resolution. There are sharp lamellar reflections on the meridian, and other reflections lie on a ser...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00350a003
更新日期:1986-01-28 00:00:00
abstract::Kinetic studies of reactions between fluorescein and antifluorescein antibody produced during early, intermediate, and late stages of the immune response have been carried out utilizing both fluorescence intensity and polarization measurements in the static (time constant similar to 5 sec) and in the stopped-flow mode...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00688a009
更新日期:1975-08-26 00:00:00
abstract::Phosphofructokinase from Escherichia coli (EcPFK) is a homotetramer with four active sites and four allosteric sites. Understanding the allosteric activation of EcPFK by MgADP has been complicated by the complex web of possible interactions, including active site homotropic interactions, allosteric site homotropic int...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi048569q
更新日期:2004-11-09 00:00:00
abstract::Perturbations within the transactivation and carboxy-terminal domains of HIV-1 Rev were examined for effects on Rev responsive element (RRE) binding activities in vitro and biological activity in vivo. Binding affinities, specificities, and multimerization of the transactivation mutants M10 and Rev/Rex M10-16 on the R...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00085a028
更新日期:1993-08-31 00:00:00
abstract::Pyruvate phosphate dikinase catalyzes the interconversion of adenosine 5'-triphosphate (ATP), orthophosphate (P(i)), and pyruvate with adenosine 5'-monophosphate (AMP), pyrophosphate (PP(i)), and phosphoenolpyruvate (PEP). The Arg 561 residue of Clostridium symbiosum PPDK is contained within a Gly-rich stretch of sequ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00007a012
更新日期:1995-02-21 00:00:00
abstract::The thylakoid transmembrane DeltapH is the sole energy source driving translocation of precursor proteins by the DeltapH/Tat machinery. Consequently, proton translocation must be coupled to precursor translocation. For the precursor of the 17 kDa protein of the oxygen-evolving complex (pOE17), the protein translocatio...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi000115f
更新日期:2000-07-18 00:00:00
abstract::Haemadin is a 57-amino acid thrombin inhibitor from the land-living leech Haemadipsa sylvestris, whose structure has recently been determined in complex with human alpha-thrombin. Here we communicate the effect of ionic strength on the kinetics of the inhibition of human alpha-thrombin by haemadin, by using thrombin m...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi011605q
更新日期:2002-02-26 00:00:00
abstract::Cold-shock proteins (Csps) are expressed at lower-than-optimum temperatures, and they function as RNA chaperones; however, no structural studies on psychrophilic Csps have been reported. Here, we aimed to investigate the structure and dynamics of the Csp of psychrophile Colwellia psychrerythraea 34H, ( Cp-Csp). Althou...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.8b00144
更新日期:2018-07-03 00:00:00