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Journal Issue - Volume 10 Issue 11 (November 2001)

Abstract The methods of continuum electrostatics are used to calculate the binding free energies of a set of protein–protein complexes including experimentally determined structures as well as other orientations generated by a fast docking algorithm. In the native structures, charged groups that are deeply buried were often found to favor complex formation (relative to isosteric nonpolar groups), whereas in nonnative complexes...

Abstract The N‐terminal SH2 domain from the p85α subunit of phosphatidylinositol 3′ kinase is cleaved specifically into 9‐ and 5‐kD fragments by limited proteolytic digestion with trypsin. The noncovalent SH2 domain complex and its constituent tryptic peptides have been investigated using high‐resolution heteronuclear magnetic resonance (NMR). These studies have established the viability of the SH2 domain as a fragment...

Abstract To assess the role of quaternary stability on the properties of Escherichia coli phosphofructokinase (PFK), a disulfide bond has been introduced across the subunit interface containing the allosteric binding sites in E. coli phosphofructokinase by changing N288 to cysteine. N288 is located in close proximity to the equivalent residue on an adjacent subunit. Although SDS‐PAGE of oxidized N288C indicates monomeric protein, blocking the...

Abstract The effects of solution conditions on protein collapse were studied by measuring the hydrodynamic radii of two unfolded proteins, α‐synuclein and acid‐denatured ferricytochrome c, in dilute solution and in 1 M glucose. The radius of α‐synuclein in dilute solution is less than that predicted for a highly denatured state, and adding 1 M glucose causes further collapse. Circular dichroic data show that α‐synuclein lacks organized ...

Abstract Two novel crystal structures of Zea mays protein kinase CK2α catalytic subunit, one in complex with the specific inhibitor 4,5,6,7‐tetrabromobenzotriazole (TBB) and another in the apo‐form, were solved at 2.2 Å resolution. These structures were compared with those of the enzyme in presence of ATP and GTP (the natural cosubstrates) and the inhibitor emodin. Interaction of TBB with the active site of CK2α is mainly due to van...

Abstract β‐Microseminoprotein, alternatively called prostatic secretory protein of 94 amino acids, is a hydrophilic, unglycosylated, small protein rich in conserved half‐cystine residues. Originally found in human seminal plasma and prostatic fluids, its presence was later shown in numerous secretions and its homologs were described in many vertebrate species. These studies showed that this protein had rapidly evolved, but they...

Abstract A peptide‐plane flip is a large‐scale rotation of the peptide plane that takes the ϕ,ψ angles at residues i and i + 1 to different structural regions in the Ramachandran plot with a comparatively small effect on the relative orientation of their side chains. This phenomenon, which is expected to play an important role during the early stages of protein folding, has been investigated using 76 proteins for which two high‐resolution X‐ray...

Abstract The three‐dimensional structure of apo‐neocarzinostatin (apo‐NCS, MW: ca.11000, antitumoral chromophore carrier protein) is based on a seven‐stranded antiparallel β‐sandwich, very similar to the immunoglobulin folding domain. We investigated the backbone dynamics of apo‐NCS by 13C‐NMR relaxation measurements and molecular dynamics simulation. Model‐free parameters determined from the experimental data are compared with a...

Abstract The transmembrane domain of the M2 protein from influenza A virus forms a nearly uniform and ideal helix in a liquid crystalline bilayer environment. The exposure of the hydrophilic backbone structure is minimized through uniform hydrogen bond geometry imposed by the low dielectric lipid environment. A high‐resolution structure of the monomer backbone and a detailed description of its orientation with respect to the bilayer...

Abstract Determination of the disulfide‐bond arrangement of a protein by characterization of disulfide‐linked peptides in proteolytic digests may be complicated by resistance of the protein to specific proteases, disulfide interchange, and/or production of extremely complex mixtures by less specific proteolysis. In this study, mass spectrometry has been used to show that incorporation of 18O into peptides during peptic digestion of...

Abstract The monomeric peptide methionine sulfoxide reductase (MsrA) catalyzes the irreversible thioredoxin‐dependent reduction of methionine sulfoxide. The crystal structure of MsrAs from Escherichia coli and Bos taurus can be described as a central core of about 140 amino acids that contains the active site. The core is wrapped by two long N‐ and C‐terminal extended chains. The catalytic mechanism of the E. coli enzyme has been recently...

Abstract The major serine proteinase inhibitor from bell pepper (Capsicum annuum, paprika) seeds was isolated, characterized, and sequenced, and its disulfide bond topology was determined. PSI‐1.2 is a 52‐amino‐acid‐long, cysteine‐rich polypeptide that inhibits both trypsin (Ki = 4.6 × 10−9 M) and chymotrypsin (Ki = 1.1 × 10−8 M) and is a circularly permuted member of the potato type II inhibitor family. Mature proteins of this family are produced ...

Abstract Spinach 5‐phospho‐d‐ribosyl α‐1‐diphosphate (PRPP) synthase isozyme 4 was synthesized in Escherichia coli and purified to near homogeneity. The activity of the enzyme is independent of Pi; it is inhibited by ADP in a competitive manner, indicating a lack of an allosteric site; and it accepts ATP, dATP, GTP, CTP, and UTP as diphosphoryl donors. All of these properties are characteristic for class II PRPP synthases. Km values for ATP and ribose...

Abstract Although bovine β‐lactoglobulin assumes a monomeric native structure at pH 3 in the absence of salt, the addition of salts stabilizes the dimer. Thermodynamics of the monomer–dimer equilibrium dependent on the salt concentration were studied by sedimentation equilibrium. The addition of NaCl, KCl, or guanidine hydrochloride below 1 M stabilized the dimer in a similar manner. On the other hand, NaClO4 was more effective than...

Abstract Hydrogen deuterium exchange, monitored by electrospray ionization mass spectrometry, has been employed to characterize structural features of a derivative of recombinant human macrophage colony stimulating factor beta (rhm‐CSFβ) in which two of the nine disulfide bridges (Cys157/Cys159–Cys′157/Cys′159) were selectively reduced and alkylated. Removal of these two disulfide bridges did not affect the biological activity of...

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