Abstract：
:The importance of a specific hydrogen bond between thermolysin and a phosphonamidate inhibitor, Z-NHCH2-PO(O-)-Leu-Leu (1) [Bartlett, P. A., & Marlowe, C. K. (1987) Science (Washington D.C.) 235, 569-571], has been reevaluated. We have determined the inhibition constants (binding free energies) for thermolysin of phosphonamidate n-hexyl-P(O)(O-)-Leu-Trp-NHMe (4), phosphonate n-hexyl-P-(O)(O-)OCH(iBu)CO-Trp-NHMe (5), and phosphinates n-hexyl-P(O)(O-)CH2CH(iBu)CO-Trp-NHMe (6) and Z-NHCH2PO(O-)CH2CH(iBu)CO-Leu (3). Replacement of the P-NH group by P-CH2 (1----3 and 4----6) weakens the overall binding free energy by about 1.5 kcal/mol. A negligible difference in solvation energy has been measured for these pairs, and the basicity of the P-O- ligand for zinc in each pair remains nearly unchanged as determined by pH titration of their 31P NMR resonances. Therefore, this value of 1.5 kcal/mol can be assigned to the specific hydrogen bond known to exist between the P-NH of 1 and thermolysin [Tronrud, D. E., Holden, H. M., & Matthews, B. W. (1987) Science (Washington, D.C.) 235, 871-574] and inferred to exist between 4 and the enzyme. Substitution of P-O for P-NH (1----2 [Bartlett, P. A., & Marlowe, C. K. (1987) Science (Washington, D.C.) 235, 569-571] and 4----5) weakens the overall binding free energy by 4.1 kcal/mol for each pair as the basicity of the P-O- ligand decreases by about 1.6 pH units. The measured solvation energy difference between 4 and 5 (and by inference between 1 and 2) is negligible.(ABSTRACT TRUNCATED AT 250 WORDS)
journal_name
Biochemistryjournal_title
Biochemistryauthors
Grobelny D,Goli UB,Galardy REdoi
10.1021/bi00438a006subject
Has Abstractpub_date
1989-06-13 00:00:00pages
4948-51issue
12eissn
0006-2960issn
1520-4995journal_volume
28pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:The transferrins (TFs) are a family of proteins that are widely distributed in vertebrates, where they serve a major role in iron binding and transport. Most TFs are composed of two homologous lobes, the N- and C-lobes, each able to bind a single iron atom. Human serum transferrin (hTF) binds iron in the blood and del...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi027071q
更新日期：2003-04-08 00:00:00
abstract：:Avian magnetoreception is assumed to occur in the retina. Although its molecular mechanism is unclear, magnetic field-dependent formation and the stability of radical-containing photointermediate(s) are suggested to play key roles in a hypothesis called the radical pair mechanism. Chicken cryptochrome4 (cCRY4) has bee...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.0c00495
更新日期：2020-09-29 00:00:00
abstract：:We have used flash-detection optical and electron paramagnetic resonance spectroscopy to measure the kinetics and yield per flash of the photooxidation of cytochrome b559 and the yield per flash of the photooxidation of the tyrosine residue YD in Mn-depleted photosystem II (PSII) membranes at room temperature. The ini...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00490a014
更新日期：1990-09-25 00:00:00
abstract：:Chicken liver phosphoenolpyruvate carboxykinase (PEPCK) was rapidly inactivated by micromolar concentrations of ferrous sulfate in the presence of ascorbate at pH 7.4. Omitting ascorbate or replacing the Fe2+ with Mn2+ or Mg2+ gives no inactivation. Mn2+, Mg2+, or Co2+ at 100-fold molar excess over Fe2+ offered comple...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi970574p
更新日期：1997-12-09 00:00:00
abstract：:We propose a simple method to find an amino acid sequence that is foldable into a globular protein with a desired structure based on a knowledge-based 3D-1D compatibility function. An asymmetric alpha-helical single-domain structure of sperm whale myoglobin consisting of 153 amino acid residues was chosen for the desi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi983006y
更新日期：1999-06-08 00:00:00
abstract：:The trans-aconitate methyltransferase from the bacterium Escherichia coli catalyzes the monomethyl esterification of trans-aconitate and related compounds. Using two-dimensional (1)H/(13)C nuclear magnetic resonance spectroscopy, we show that the methylation is specific to one of the three carboxyl groups and further ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0022902
更新日期：2001-02-20 00:00:00
abstract：:Locusta migratoria apolipophorin III (apoLp-III) is a helix bundle exchangeable apolipoprotein that reversibly binds to lipoprotein surfaces. Structural reorganization of its five amphipathic alpha-helices enables the transition from the lipid-free to lipid-bound state. ApoLp-III-induced transformation of dimyristoylp...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi010410f
更新日期：2001-06-26 00:00:00
abstract：:The kinetics and energetics of the binding between barley alpha-amylase/subtilisin inhibitor (BASI) or BASI mutants and barley alpha-amylase 2 (AMY2) were determined using surface plasmon resonance and isothermal titration calorimetry (ITC). Binding kinetics were in accordance with a 1:1 binding model. At pH 5.5, [Ca(...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi020508+
更新日期：2003-02-18 00:00:00
abstract：:Bacteriophage T7 codes for a single-stranded DNA binding protein. This protein is the product of gene 2.5 and has been found previously to stimulate specifically the activity of the phage-coded DNA polymerase. We report here that the T7 DNA binding protein also stimulates the activity of the phage-coded exonuclease. T...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00266a042
更新日期：1982-11-09 00:00:00
abstract：:In Escherichia coli, the cyclic AMP receptor protein (CRP) serves as a sensor of the intracellular level of cyclic AMP. At increasing concentrations of cyclic AMP, CRP becomes activated upon binding a cyclic AMP molecule. The activated CRP is capable of regulating the expression of more than 20 genes by binding to spe...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi972450i
更新日期：1998-04-14 00:00:00
abstract：:The linkage between substrate and regulatory effector binding to separate sites on allosteric enzymes results in shifts in their sigmoidal kinetics to regulate metabolism. Control of branched chain amino acid biosynthesis in Escherichia coli occurs in part through shifts in the sigmoidal dependence of alpha-ketobutyra...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00029a016
更新日期：1995-07-25 00:00:00
abstract：:The Cyt toxins produced by the bacteria Bacillus thuringiensis show insecticidal activity against some insects, mainly dipteran larvae, being able to kill mosquitoes and black flies. However, they also possess a general cytolytic activity in vitro, showing hemolytic activity in red blood cells. These proteins are comp...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi101239r
更新日期：2011-01-25 00:00:00
abstract：:These investigations characterize the covalent binding of reactive products of prostaglandin H-synthases (PGHSs) to the enzyme and to other molecules. The intermediate product of oxygenation of arachidonic acid by the PGHSs, prostaglandin (PG) H2, undergoes rearrangement to the highly reactive gamma-keto aldehydes, le...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi002629k
更新日期：2001-06-12 00:00:00
abstract：:Adriamycin plays a prominent role in the treatment of leukemia and solid tumors in man. The mode of interaction of adriamycin with its nuclear target, responsible for its therapeutic effect, is known [Berman, H. M., & Young, P.R. (1981) Annu. Rev. Biophys. Bioeng. 10, 87-114]. The planar anthracycline moiety of adriam...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00380a043
更新日期：1987-03-24 00:00:00
abstract：:RNAs are involved in myriad cellular events. In general, RNA function is affected by cellular conditions. For instance, molecular crowding promotes RNA folding through compaction of the RNA. Metabolites generally destabilize RNA secondary structure, which improves RNA folding cooperativity and increases the fraction o...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.9b00578
更新日期：2019-09-24 00:00:00
abstract：:The spontaneous hydrolyses of lactic acid O-phenyl phosphate (I) and, to a lesser extent, 3-hydroxybutyric acid O-phenyl phosphate (II) have been investigated and compared with similar intramolecular and bimolecular reactions. Compared to bimolecular nucleophilic reactions, the reactivity of II is similar to other sys...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00682a025
更新日期：1975-06-03 00:00:00
abstract：:To be fully active and participate in the metabolism of phosphorylated nucleotides, most nucleoside diphosphate kinases (NDPKs) have to assemble into stable hexamers. Here we studied the role played by six intersubunit salt bridges R80-D93 in the stability of NDPK from the pathogen Mycobacterium tuberculosis ( Mt). Mu...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.8b01308
更新日期：2019-03-12 00:00:00
abstract：:The bacterial reaction center (RC) converts light into chemical energy through the reduction of an internal quinone molecule Q(B) to Q(B)H(2). In the native RC, proton transfer is coupled to electron transfer and is not rate-controlling. Consequently, proton transfer is not directly observable, and its rate was unknow...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi020419x
更新日期：2002-12-17 00:00:00
abstract：:Spectroscopic characterization of the newly discovered heme-PAS domain sensor protein BxRcoM-2 reveals that this protein undergoes redox-dependent ligand switching and CO- and NO-induced ligand displacement. The aerobic bacterium Burkholderia xenovorans expresses two homologous heme-containing proteins that promote CO...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi800486x
更新日期：2008-08-26 00:00:00
abstract：:The antiviral and antiproliferative activities of type I interferons (IFNs) are mediated by a common receptor, and its second subunit (IFNAR2) exhibits nanomolar affinity to both IFNalpha and IFNbeta subtypes. We have previously determined the structure of the IFN-binding extracellular domain of IFNAR2 (IFNAR2-EC) usi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi049606g
更新日期：2004-08-10 00:00:00
abstract：:Recognition for proteolysis by trypsin depends almost exclusively on tight binding of arginine or lysine side chains by the primary substrate specificity pocket. Although extended subsite interactions are important for catalysis, the majority of binding energy is localized in the P1 pocket. Analysis of the interaction...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9530191
更新日期：1996-05-14 00:00:00
abstract：:In recent years, there has been dramatic growth in the study of RNA. RNA has gone from being known as an intermediate in the central dogma of molecular biology to a molecule with a large diversity of structure and function that is involved in all aspects of biology. As new functions are rapidly discovered, it has beco...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.7b01141
更新日期：2018-08-07 00:00:00
abstract：:Misaligned structures can result from strand slippage during DNA replication and, if not repaired, would lead to mutations. Previously, we showed that strand slippage can occur upon misincorporation of a dNTP opposite thymine and cytosine templates, resulting in a misaligned structure with a T- or C-bulge. The formati...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9014049
更新日期：2009-12-08 00:00:00
abstract：:An improved procedure for the preparation of cobalt-cytochrome c has been developed. Various factors influencing the cobalt insertion process are discussed. The optical spectra of cobalt-cytochrome c suggest a six-coordinated species. The spectral shifts occurring with oxidation-reduction are compared with those obser...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00687a003
更新日期：1975-08-12 00:00:00
abstract：:Experimental and theoretical double-mutant cycles have been used to investigate a salt bridge in the N-terminal domain of the protein L9. Aspartic acid 23 is the only acidic residue involved in a well-defined pairwise interaction, namely, a partially solvent-exposed salt bridge with the protonated N-terminus of the pr...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi027202n
更新日期：2003-06-17 00:00:00
abstract：:Class II MHC glycoproteins bind short (7-25 amino acid) peptides in an extended type II polyproline-like conformation and present them for immune recognition. Because empty MHC is unstable, measurement of the rate of the second-order reaction between peptide and MHC is challenging. In this report, we use dissociation ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9921337
更新日期：2000-02-08 00:00:00
abstract：:The hairpin ribozyme is an RNA enzyme that performs site-specific phosphodiester bond cleavage between nucleotides A-1 and G+1 within its cognate substrate. Previous functional studies revealed that the minimal hairpin ribozyme exhibited "gain-of-function" cleavage properties resulting from U39C or U39 to propyl linke...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi051550i
更新日期：2005-11-08 00:00:00
abstract：:N1-(5'-Phosphoribosyl)adenosine-5'-monophosphate cyclohydrolase (HisI, PR-AMP cyclohydrolase) is a central enzyme in histidine biosynthesis catalyzing the hydrolysis of the N1-C6 bond of the purine substrate, a reaction unique to this pathway. A source of the recombinant monofunctional Methanococcus vannielii PR-AMP c...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi982475x
更新日期：1999-02-02 00:00:00
abstract：:Unoccupied estrogen receptor (ER) can be extracted from tissues by homogenization with a hypotonic buffer, whereas hormone-occupied ER becomes tightly bound to the nuclear pellet and must be extracted with high-salt-containing buffers. The molecular basis for estrogen-induced tight nuclear binding of ER remains an imp...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi982190k
更新日期：1999-06-01 00:00:00
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 intermed...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi000357f
更新日期：2000-07-11 00:00:00
